rs16856462
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_052934.4(SLC26A9):āc.2243A>Gā(p.His748Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 1,612,986 control chromosomes in the GnomAD database, including 5,749 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_052934.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A9 | NM_052934.4 | c.2243A>G | p.His748Arg | missense_variant | 19/21 | ENST00000367135.8 | |
SLC26A9 | NM_134325.3 | c.2243A>G | p.His748Arg | missense_variant | 19/22 | ||
SLC26A9 | XM_011509121.3 | c.1976A>G | p.His659Arg | missense_variant | 18/20 | ||
SLC26A9 | XM_011509122.3 | c.1751A>G | p.His584Arg | missense_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A9 | ENST00000367135.8 | c.2243A>G | p.His748Arg | missense_variant | 19/21 | 1 | NM_052934.4 | P1 | |
SLC26A9 | ENST00000340781.8 | c.2243A>G | p.His748Arg | missense_variant | 18/21 | 1 | |||
SLC26A9 | ENST00000367134.2 | c.2243A>G | p.His748Arg | missense_variant | 19/22 | 5 | |||
SLC26A9 | ENST00000491127.5 | n.1627A>G | non_coding_transcript_exon_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0989 AC: 15044AN: 152108Hom.: 916 Cov.: 33
GnomAD3 exomes AF: 0.0718 AC: 18044AN: 251402Hom.: 882 AF XY: 0.0700 AC XY: 9512AN XY: 135868
GnomAD4 exome AF: 0.0767 AC: 111996AN: 1460760Hom.: 4829 Cov.: 31 AF XY: 0.0758 AC XY: 55073AN XY: 726544
GnomAD4 genome ? AF: 0.0990 AC: 15067AN: 152226Hom.: 920 Cov.: 33 AF XY: 0.0946 AC XY: 7039AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at