chrX-19537724-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_031892.3(SH3KBP1):c.1949G>A(p.Arg650Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00623 in 1,208,947 control chromosomes in the GnomAD database, including 26 homozygotes. There are 2,542 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R650W) has been classified as Uncertain significance.
Frequency
Consequence
NM_031892.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3KBP1 | NM_031892.3 | c.1949G>A | p.Arg650Gln | missense_variant | 17/18 | ENST00000397821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3KBP1 | ENST00000397821.8 | c.1949G>A | p.Arg650Gln | missense_variant | 17/18 | 1 | NM_031892.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00442 AC: 493AN: 111461Hom.: 0 Cov.: 23 AF XY: 0.00431 AC XY: 145AN XY: 33651
GnomAD3 exomes AF: 0.00443 AC: 812AN: 183337Hom.: 4 AF XY: 0.00506 AC XY: 343AN XY: 67777
GnomAD4 exome AF: 0.00642 AC: 7043AN: 1097435Hom.: 26 Cov.: 29 AF XY: 0.00661 AC XY: 2397AN XY: 362829
GnomAD4 genome ? AF: 0.00441 AC: 492AN: 111512Hom.: 0 Cov.: 23 AF XY: 0.00430 AC XY: 145AN XY: 33712
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at