22-37639806-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018957.6(SH3BP1):c.19C>T(p.His7Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000446 in 1,568,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3BP1 | NM_018957.6 | c.19C>T | p.His7Tyr | missense_variant | Exon 1 of 18 | ENST00000649765.2 | NP_061830.3 | |
SH3BP1 | NM_001350055.2 | c.19C>T | p.His7Tyr | missense_variant | Exon 1 of 18 | NP_001336984.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3BP1 | ENST00000649765.2 | c.19C>T | p.His7Tyr | missense_variant | Exon 1 of 18 | NM_018957.6 | ENSP00000497104.1 | |||
ENSG00000285304 | ENST00000451997 | c.-131C>T | 5_prime_UTR_variant | Exon 1 of 17 | 2 | ENSP00000401076.2 | ||||
SH3BP1 | ENST00000417536.5 | n.19C>T | non_coding_transcript_exon_variant | Exon 2 of 20 | 2 | ENSP00000411979.1 | ||||
SH3BP1 | ENST00000644149.1 | n.112C>T | non_coding_transcript_exon_variant | Exon 1 of 17 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1416434Hom.: 0 Cov.: 31 AF XY: 0.00000285 AC XY: 2AN XY: 701892
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19C>T (p.H7Y) alteration is located in exon 1 (coding exon 1) of the SH3BP1 gene. This alteration results from a C to T substitution at nucleotide position 19, causing the histidine (H) at amino acid position 7 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at