VCV000708551.6 - ClinVar

NM_006885.4(ZFHX3):c.2915C>T (p.Ser972Leu)

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Benign

1 out of 2 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006885.4(ZFHX3):c.2915C>T (p.Ser972Leu)

Variation ID: 708551 Accession: VCV000708551.6

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 16q22.3 16: 72950770 (GRCh38) [ NCBI UCSC ] 16: 72984669 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 17, 2019	Oct 8, 2024	Dec 31, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NM_006885.4:c.2915C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_008816.3:p.Ser972Leu	missense
NM_001164766.2:c.173C>T	NP_001158238.1:p.Ser58Leu	missense
NC_000016.10:g.72950770G>A
NC_000016.9:g.72984669G>A
NG_013211.2:g.946162C>T

... more HGVS ... less HGVS

Protein change

S58L, S972L

Other names

Canonical SPDI

NC_000016.10:72950769:G:A

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00599 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015

Trans-Omics for Precision Medicine (TOPMed) 0.00101

The Genome Aggregation Database (gnomAD), exomes 0.00278

The Genome Aggregation Database (gnomAD) 0.00379

The Genome Aggregation Database (gnomAD) 0.00399

Exome Aggregation Consortium (ExAC) 0.00485

1000 Genomes Project 30x 0.00515

The Genome Aggregation Database (gnomAD), exomes 0.00534

1000 Genomes Project 0.00599

Links

ClinGen: CA8164252 dbSNP: rs77124117 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ZFHX3		-	-	GRCh38 GRCh37	336	984

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Benign (1)	criteria provided, single submitter	Dec 31, 2019	RCV000879831.5
ZFHX3-related disorder	Benign (1)	no assertion criteria provided	Jun 13, 2019	RCV003940390.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Dec 31, 2019) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	not provided	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001022884.2 First in ClinVar: Dec 17, 2019 Last updated: May 04, 2020	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Benign (Jun 13, 2019) N Not contributing to aggregate classification	no assertion criteria provided	ZFHX3-related condition	PreventionGenetics, part of Exact Sciences Accession: SCV004751315.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: show This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs77124117 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 17, 2025