chr17-39965740-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178171.5(GSDMA):c.53G>A(p.Arg18Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,609,784 control chromosomes in the GnomAD database, including 162,085 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_178171.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSDMA | NM_178171.5 | c.53G>A | p.Arg18Gln | missense_variant | 2/12 | ENST00000301659.9 | |
GSDMA | XM_006721832.4 | c.53G>A | p.Arg18Gln | missense_variant | 2/12 | ||
GSDMA | XM_017024502.3 | c.53G>A | p.Arg18Gln | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSDMA | ENST00000301659.9 | c.53G>A | p.Arg18Gln | missense_variant | 2/12 | 1 | NM_178171.5 | P1 | |
GSDMA | ENST00000635792.1 | c.53G>A | p.Arg18Gln | missense_variant | 2/12 | 5 | P1 | ||
GSDMA | ENST00000577447.1 | c.53G>A | p.Arg18Gln | missense_variant | 2/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.413 AC: 62613AN: 151754Hom.: 13327 Cov.: 30
GnomAD3 exomes AF: 0.458 AC: 111394AN: 243136Hom.: 25996 AF XY: 0.455 AC XY: 59939AN XY: 131808
GnomAD4 exome AF: 0.450 AC: 655883AN: 1457912Hom.: 148765 Cov.: 47 AF XY: 0.450 AC XY: 326090AN XY: 724894
GnomAD4 genome AF: 0.412 AC: 62610AN: 151872Hom.: 13320 Cov.: 30 AF XY: 0.411 AC XY: 30504AN XY: 74216
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at