3-32165835-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_015141.4(GPD1L):c.981G>A(p.Val327Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000346 in 1,601,564 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015141.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPD1L | ENST00000282541.10 | c.981G>A | p.Val327Val | synonymous_variant | Exon 8 of 8 | 1 | NM_015141.4 | ENSP00000282541.6 | ||
GPD1L | ENST00000474846.5 | n.905G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
GPD1L | ENST00000496151.1 | n.482G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00177 AC: 270AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000529 AC: 133AN: 251460Hom.: 0 AF XY: 0.000419 AC XY: 57AN XY: 135902
GnomAD4 exome AF: 0.000192 AC: 278AN: 1449280Hom.: 3 Cov.: 27 AF XY: 0.000190 AC XY: 137AN XY: 721906
GnomAD4 genome AF: 0.00181 AC: 276AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.00185 AC XY: 138AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:4
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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GPD1L-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Brugada syndrome 2 Benign:1
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Brugada syndrome Benign:1
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Cardiovascular phenotype 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