3-15256289-CTTCTGCCCTGTCTCCTATAGAAATACAAGGATTATCAAAAGTGAGTATTGACAA-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_004844.5(SH3BP5):c.1151-40_1164del variant causes a splice acceptor, coding sequence, intron change. The variant allele was found at a frequency of 0.00239 in 152,270 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 3 hom. )
Failed GnomAD Quality Control
Consequence
SH3BP5
NM_004844.5 splice_acceptor, coding_sequence, intron
NM_004844.5 splice_acceptor, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.90
Genes affected
SH3BP5 (HGNC:10827): (SH3 domain binding protein 5) Enables guanyl-nucleotide exchange factor activity and protein kinase inhibitor activity. Acts upstream of or within intracellular signal transduction. Located in cytoplasmic vesicle membrane and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 3-15256289-CTTCTGCCCTGTCTCCTATAGAAATACAAGGATTATCAAAAGTGAGTATTGACAA-C is Benign according to our data. Variant chr3-15256289-CTTCTGCCCTGTCTCCTATAGAAATACAAGGATTATCAAAAGTGAGTATTGACAA-C is described in ClinVar as [Likely_benign]. Clinvar id is 735908.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP5 | NM_004844.5 | c.1151-40_1164del | splice_acceptor_variant, coding_sequence_variant, intron_variant | 9/9 | ENST00000383791.8 | ||
SH3BP5-AS1 | NR_046084.1 | n.2135_2188del | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP5 | ENST00000383791.8 | c.1151-40_1164del | splice_acceptor_variant, coding_sequence_variant, intron_variant | 9/9 | 1 | NM_004844.5 | P1 | ||
SH3BP5-AS1 | ENST00000420195.1 | n.2135_2188del | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00238 AC: 362AN: 152152Hom.: 2 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000300 AC: 438AN: 1461804Hom.: 3 AF XY: 0.000285 AC XY: 207AN XY: 727206
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GnomAD4 genome AF: 0.00239 AC: 364AN: 152270Hom.: 2 Cov.: 32 AF XY: 0.00246 AC XY: 183AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at