15-83576674-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_003027.5(SH3GL3):c.557C>T(p.Ala186Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,732 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 (★).
Frequency
Consequence
NM_003027.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3GL3 | ENST00000427482.7 | c.557C>T | p.Ala186Val | missense_variant | Exon 6 of 9 | 1 | NM_003027.5 | ENSP00000391372.2 | ||
SH3GL3 | ENST00000563901.5 | n.*352C>T | non_coding_transcript_exon_variant | Exon 6 of 9 | 1 | ENSP00000456249.1 | ||||
SH3GL3 | ENST00000563901.5 | n.*352C>T | 3_prime_UTR_variant | Exon 6 of 9 | 1 | ENSP00000456249.1 | ||||
SH3GL3 | ENST00000324537.5 | c.581C>T | p.Ala194Val | missense_variant | Exon 9 of 12 | 2 | ENSP00000320092.5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151816Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251028Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135694
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460916Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726832
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151816Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74106
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.557C>T (p.A186V) alteration is located in exon 6 (coding exon 6) of the SH3GL3 gene. This alteration results from a C to T substitution at nucleotide position 557, causing the alanine (A) at amino acid position 186 to be replaced by a valine (V). 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