chr2-235041274-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014521.3(SH3BP4):c.505C>T(p.Pro169Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P169A) has been classified as Uncertain significance.
Frequency
Consequence
NM_014521.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP4 | NM_014521.3 | c.505C>T | p.Pro169Ser | missense_variant | 4/6 | ENST00000392011.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP4 | ENST00000392011.7 | c.505C>T | p.Pro169Ser | missense_variant | 4/6 | 1 | NM_014521.3 | P1 | |
SH3BP4 | ENST00000344528.8 | c.505C>T | p.Pro169Ser | missense_variant | 4/6 | 1 | P1 | ||
SH3BP4 | ENST00000409212.5 | c.505C>T | p.Pro169Ser | missense_variant | 4/6 | 5 | P1 | ||
SH3BP4 | ENST00000446904.5 | c.505C>T | p.Pro169Ser | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461874Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.505C>T (p.P169S) alteration is located in exon 4 (coding exon 2) of the SH3BP4 gene. This alteration results from a C to T substitution at nucleotide position 505, causing the proline (P) at amino acid position 169 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.