19-2334713-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152988.3(SPPL2B):āc.178A>Gā(p.Ser60Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000841 in 1,604,284 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_152988.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPPL2B | NM_152988.3 | c.178A>G | p.Ser60Gly | missense_variant | 2/15 | ENST00000613503.5 | |
SPPL2B | NM_001077238.2 | c.178A>G | p.Ser60Gly | missense_variant | 2/15 | ||
SPPL2B | XM_011528138.3 | c.178A>G | p.Ser60Gly | missense_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPPL2B | ENST00000613503.5 | c.178A>G | p.Ser60Gly | missense_variant | 2/15 | 1 | NM_152988.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000162 AC: 38AN: 234472Hom.: 1 AF XY: 0.000180 AC XY: 23AN XY: 127774
GnomAD4 exome AF: 0.0000723 AC: 105AN: 1452118Hom.: 2 Cov.: 31 AF XY: 0.0000693 AC XY: 50AN XY: 721772
GnomAD4 genome AF: 0.000197 AC: 30AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74350
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at