7-107674313-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: The filtering allele frequency of the p.Ala1898Ser variant in the SLC26A4 gene is 1.2% (324/24040) of African chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA132732/MONDO:0010134/005
Frequency
Consequence
NM_000441.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00347 AC: 528AN: 152134Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 264AN: 251448Hom.: 4 AF XY: 0.000625 AC XY: 85AN XY: 135898
GnomAD4 exome AF: 0.000330 AC: 482AN: 1461622Hom.: 3 Cov.: 31 AF XY: 0.000271 AC XY: 197AN XY: 727146
GnomAD4 genome AF: 0.00347 AC: 528AN: 152252Hom.: 6 Cov.: 32 AF XY: 0.00332 AC XY: 247AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 07, 2025 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 15, 2019 | This variant is associated with the following publications: (PMID: 25262649, 17309986, 27771369, 30245029, 30068397) - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | SLC26A4: BS1 - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 14, 2011 | Ala189Ser in exon 5 of SLC26A4: This variant is not expected to have clinical si gnificance because it has been identified in 0.38% (25/6628) of chromosomes from a broad population (dbSNP rs35045430). - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 05, 2016 | - - |
Pendred syndrome Benign:2
Benign, reviewed by expert panel | curation | ClinGen Hearing Loss Variant Curation Expert Panel | Sep 28, 2018 | The filtering allele frequency of the p.Ala1898Ser variant in the SLC26A4 gene is 1.2% (324/24040) of African chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 02, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at