chr2-235041298-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014521.3(SH3BP4):c.529G>A(p.Val177Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014521.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP4 | NM_014521.3 | c.529G>A | p.Val177Ile | missense_variant | 4/6 | ENST00000392011.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP4 | ENST00000392011.7 | c.529G>A | p.Val177Ile | missense_variant | 4/6 | 1 | NM_014521.3 | P1 | |
SH3BP4 | ENST00000344528.8 | c.529G>A | p.Val177Ile | missense_variant | 4/6 | 1 | P1 | ||
SH3BP4 | ENST00000409212.5 | c.529G>A | p.Val177Ile | missense_variant | 4/6 | 5 | P1 | ||
SH3BP4 | ENST00000446904.5 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251308Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135854
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461868Hom.: 0 Cov.: 35 AF XY: 0.0000509 AC XY: 37AN XY: 727232
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.529G>A (p.V177I) alteration is located in exon 4 (coding exon 2) of the SH3BP4 gene. This alteration results from a G to A substitution at nucleotide position 529, causing the valine (V) at amino acid position 177 to be replaced by an isoleucine (I). 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