chr3-15256306-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004844.5(SH3BP5):c.1151-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00461 in 1,611,884 control chromosomes in the GnomAD database, including 253 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004844.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP5 | NM_004844.5 | c.1151-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000383791.8 | |||
SH3BP5-AS1 | NR_046084.1 | n.2123A>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP5 | ENST00000383791.8 | c.1151-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004844.5 | P1 | |||
SH3BP5-AS1 | ENST00000420195.1 | n.2123A>G | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0255 AC: 3864AN: 151364Hom.: 139 Cov.: 32
GnomAD3 exomes AF: 0.00642 AC: 1595AN: 248634Hom.: 59 AF XY: 0.00441 AC XY: 594AN XY: 134598
GnomAD4 exome AF: 0.00244 AC: 3563AN: 1460406Hom.: 113 Cov.: 30 AF XY: 0.00213 AC XY: 1544AN XY: 726562
GnomAD4 genome AF: 0.0256 AC: 3872AN: 151478Hom.: 140 Cov.: 32 AF XY: 0.0241 AC XY: 1782AN XY: 74036
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at