2-235041274-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014521.3(SH3BP4):āc.505C>Gā(p.Pro169Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,040 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P169S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014521.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP4 | NM_014521.3 | c.505C>G | p.Pro169Ala | missense_variant | 4/6 | ENST00000392011.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP4 | ENST00000392011.7 | c.505C>G | p.Pro169Ala | missense_variant | 4/6 | 1 | NM_014521.3 | P1 | |
SH3BP4 | ENST00000344528.8 | c.505C>G | p.Pro169Ala | missense_variant | 4/6 | 1 | P1 | ||
SH3BP4 | ENST00000409212.5 | c.505C>G | p.Pro169Ala | missense_variant | 4/6 | 5 | P1 | ||
SH3BP4 | ENST00000446904.5 | c.505C>G | p.Pro169Ala | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251386Hom.: 1 AF XY: 0.0000221 AC XY: 3AN XY: 135888
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461874Hom.: 2 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 727240
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.505C>G (p.P169A) alteration is located in exon 4 (coding exon 2) of the SH3BP4 gene. This alteration results from a C to G substitution at nucleotide position 505, causing the proline (P) at amino acid position 169 to be replaced by an alanine (A). 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