17-39971569-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_178171.5(GSDMA):c.604G>A(p.Val202Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,962 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V202A) has been classified as Uncertain significance.
Frequency
Consequence
NM_178171.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSDMA | NM_178171.5 | c.604G>A | p.Val202Ile | missense_variant | Exon 5 of 12 | ENST00000301659.9 | NP_835465.2 | |
GSDMA | XM_006721832.4 | c.604G>A | p.Val202Ile | missense_variant | Exon 5 of 12 | XP_006721895.1 | ||
GSDMA | XM_017024502.3 | c.604G>A | p.Val202Ile | missense_variant | Exon 5 of 11 | XP_016879991.1 | ||
GSDMA | XM_011524651.4 | c.178G>A | p.Val60Ile | missense_variant | Exon 3 of 10 | XP_011522953.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000177 AC: 44AN: 249200Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135188
GnomAD4 exome AF: 0.000111 AC: 162AN: 1461660Hom.: 1 Cov.: 30 AF XY: 0.000165 AC XY: 120AN XY: 727112
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at