rs117444825
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198999.3(SLC26A5):āc.989A>Gā(p.Asn330Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 1,613,928 control chromosomes in the GnomAD database, including 262 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N330D) has been classified as Likely benign.
Frequency
Consequence
NM_198999.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC26A5 | NM_198999.3 | c.989A>G | p.Asn330Ser | missense_variant | 10/20 | ENST00000306312.8 | NP_945350.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A5 | ENST00000306312.8 | c.989A>G | p.Asn330Ser | missense_variant | 10/20 | 1 | NM_198999.3 | ENSP00000304783.3 | ||
SLC26A5 | ENST00000393727.5 | c.989A>G | p.Asn330Ser | missense_variant | 8/18 | 1 | ENSP00000377328.1 | |||
SLC26A5 | ENST00000393723.2 | c.989A>G | p.Asn330Ser | missense_variant | 8/17 | 1 | ENSP00000377324.1 |
Frequencies
GnomAD3 genomes AF: 0.00949 AC: 1444AN: 152162Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00978 AC: 2457AN: 251122Hom.: 20 AF XY: 0.00960 AC XY: 1303AN XY: 135732
GnomAD4 exome AF: 0.0169 AC: 24638AN: 1461648Hom.: 253 Cov.: 31 AF XY: 0.0161 AC XY: 11677AN XY: 727138
GnomAD4 genome AF: 0.00948 AC: 1444AN: 152280Hom.: 9 Cov.: 32 AF XY: 0.00877 AC XY: 653AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 20, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 13, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Asn330Ser in Exon 10 of SLC26A5: This variant is not expected to have clinical s ignificance because it has been identified in 1.7% (121/7020) of European Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs117444825). - |
Autosomal recessive nonsyndromic hearing loss 61 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 20, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at