chr7-80478905-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001102386.3(GNAT3):c.397G>A(p.Asp133Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,613,384 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001102386.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000225 AC: 56AN: 248818Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 135006
GnomAD4 exome AF: 0.000179 AC: 262AN: 1461134Hom.: 1 Cov.: 30 AF XY: 0.000171 AC XY: 124AN XY: 726836
GnomAD4 genome AF: 0.000158 AC: 24AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.397G>A (p.D133N) alteration is located in exon 4 (coding exon 4) of the GNAT3 gene. This alteration results from a G to A substitution at nucleotide position 397, causing the aspartic acid (D) at amino acid position 133 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