chr5-172347268-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001017995.3(SH3PXD2B):c.1062+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00422 in 1,613,954 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001017995.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3PXD2B | NM_001017995.3 | c.1062+15G>A | intron_variant | Intron 11 of 12 | ENST00000311601.6 | NP_001017995.1 | ||
SH3PXD2B | NM_001308175.2 | c.1062+15G>A | intron_variant | Intron 11 of 12 | NP_001295104.1 | |||
SH3PXD2B | XM_017009351.2 | c.1146+15G>A | intron_variant | Intron 12 of 13 | XP_016864840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3PXD2B | ENST00000311601.6 | c.1062+15G>A | intron_variant | Intron 11 of 12 | 1 | NM_001017995.3 | ENSP00000309714.5 | |||
SH3PXD2B | ENST00000519643.5 | c.1062+15G>A | intron_variant | Intron 11 of 12 | 1 | ENSP00000430890.1 | ||||
SH3PXD2B | ENST00000636523.1 | c.1101+15G>A | intron_variant | Intron 12 of 13 | 5 | ENSP00000490082.1 | ||||
SH3PXD2B | ENST00000518522.5 | c.72+15G>A | intron_variant | Intron 2 of 3 | 5 | ENSP00000428076.1 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2335AN: 152106Hom.: 57 Cov.: 32
GnomAD3 exomes AF: 0.00535 AC: 1346AN: 251440Hom.: 23 AF XY: 0.00464 AC XY: 630AN XY: 135900
GnomAD4 exome AF: 0.00306 AC: 4469AN: 1461730Hom.: 43 Cov.: 30 AF XY: 0.00295 AC XY: 2145AN XY: 727182
GnomAD4 genome AF: 0.0153 AC: 2336AN: 152224Hom.: 57 Cov.: 32 AF XY: 0.0147 AC XY: 1093AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:1
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Frank-Ter Haar syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at