chr17-39976981-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178171.5(GSDMA):c.1261G>A(p.Asp421Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178171.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSDMA | NM_178171.5 | c.1261G>A | p.Asp421Asn | missense_variant | 12/12 | ENST00000301659.9 | |
GSDMA | XM_006721832.4 | c.1261G>A | p.Asp421Asn | missense_variant | 12/12 | ||
GSDMA | XM_017024502.3 | c.1234G>A | p.Asp412Asn | missense_variant | 11/11 | ||
GSDMA | XM_011524651.4 | c.835G>A | p.Asp279Asn | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSDMA | ENST00000301659.9 | c.1261G>A | p.Asp421Asn | missense_variant | 12/12 | 1 | NM_178171.5 | P1 | |
GSDMA | ENST00000635792.1 | c.1261G>A | p.Asp421Asn | missense_variant | 12/12 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152136Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249258Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135224
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727136
GnomAD4 genome AF: 0.000151 AC: 23AN: 152254Hom.: 0 Cov.: 31 AF XY: 0.000201 AC XY: 15AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.1261G>A (p.D421N) alteration is located in exon 12 (coding exon 11) of the GSDMA gene. This alteration results from a G to A substitution at nucleotide position 1261, causing the aspartic acid (D) at amino acid position 421 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