1-38875089-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_030772.5(GJA9):c.1010G>A(p.Ser337Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000642 in 1,614,092 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030772.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJA9 | NM_030772.5 | c.1010G>A | p.Ser337Asn | missense_variant | Exon 2 of 2 | ENST00000357771.5 | NP_110399.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJA9 | ENST00000357771.5 | c.1010G>A | p.Ser337Asn | missense_variant | Exon 2 of 2 | 1 | NM_030772.5 | ENSP00000350415.3 | ||
ENSG00000274944 | ENST00000621281.1 | c.37-1999G>A | intron_variant | Intron 1 of 4 | 2 | ENSP00000479064.1 |
Frequencies
GnomAD3 genomes AF: 0.000592 AC: 90AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000613 AC: 154AN: 251272Hom.: 1 AF XY: 0.000589 AC XY: 80AN XY: 135862
GnomAD4 exome AF: 0.000648 AC: 948AN: 1461852Hom.: 4 Cov.: 35 AF XY: 0.000701 AC XY: 510AN XY: 727224
GnomAD4 genome AF: 0.000585 AC: 89AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1010G>A (p.S337N) alteration is located in exon 2 (coding exon 1) of the GJA9 gene. This alteration results from a G to A substitution at nucleotide position 1010, causing the serine (S) at amino acid position 337 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at