chr7-107767592-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000111.3(SLC26A3):c.2258A>G(p.Asn753Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,607,962 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000111.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC26A3 | NM_000111.3 | c.2258A>G | p.Asn753Ser | missense_variant | 20/21 | ENST00000340010.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A3 | ENST00000340010.10 | c.2258A>G | p.Asn753Ser | missense_variant | 20/21 | 1 | NM_000111.3 | P1 | |
SLC26A3 | ENST00000379083.7 | c.*1815A>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00804 AC: 1223AN: 152166Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.00199 AC: 500AN: 250830Hom.: 4 AF XY: 0.00156 AC XY: 212AN XY: 135598
GnomAD4 exome AF: 0.000794 AC: 1156AN: 1455678Hom.: 11 Cov.: 29 AF XY: 0.000662 AC XY: 480AN XY: 724624
GnomAD4 genome ? AF: 0.00807 AC: 1229AN: 152284Hom.: 20 Cov.: 32 AF XY: 0.00767 AC XY: 571AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 14, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Congenital secretory diarrhea, chloride type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at