rs72546650
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000282541.10(GPD1L):c.366+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,613,620 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000282541.10 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPD1L | NM_015141.4 | c.366+8G>A | splice_region_variant, intron_variant | ENST00000282541.10 | NP_055956.1 | |||
GPD1L | XM_006713068.3 | c.226-1493G>A | intron_variant | XP_006713131.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPD1L | ENST00000282541.10 | c.366+8G>A | splice_region_variant, intron_variant | 1 | NM_015141.4 | ENSP00000282541 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00588 AC: 894AN: 152088Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00164 AC: 410AN: 250666Hom.: 2 AF XY: 0.00123 AC XY: 166AN XY: 135466
GnomAD4 exome AF: 0.000620 AC: 906AN: 1461414Hom.: 5 Cov.: 32 AF XY: 0.000523 AC XY: 380AN XY: 727032
GnomAD4 genome AF: 0.00591 AC: 900AN: 152206Hom.: 11 Cov.: 32 AF XY: 0.00579 AC XY: 431AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2014 | 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. - |
Brugada syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at