chr15-41851090-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016642.4(SPTBN5):c.10804C>T(p.Arg3602Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,612,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3602L) has been classified as Uncertain significance.
Frequency
Consequence
NM_016642.4 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 |
---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10804C>T | p.Arg3602Cys | missense_variant | 65/68 | ENST00000320955.8 | |
SPTBN5 | XM_017022299.2 | c.10984C>T | p.Arg3662Cys | missense_variant | 63/66 | ||
SPTBN5 | XM_017022302.2 | c.8161C>T | p.Arg2721Cys | missense_variant | 51/54 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN5 | ENST00000320955.8 | c.10804C>T | p.Arg3602Cys | missense_variant | 65/68 | 1 | NM_016642.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000728 AC: 18AN: 247088Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134506
GnomAD4 exome AF: 0.0000801 AC: 117AN: 1460608Hom.: 0 Cov.: 36 AF XY: 0.0000757 AC XY: 55AN XY: 726584
GnomAD4 genome ? AF: 0.0000656 AC: 10AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74518
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 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