chr15-41851335-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016642.4(SPTBN5):c.10691A>C(p.Asn3564Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 1,550,786 control chromosomes in the GnomAD database, including 610,980 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_016642.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10691A>C | p.Asn3564Thr | missense_variant | 64/68 | ENST00000320955.8 | |
SPTBN5 | XM_017022299.2 | c.10871A>C | p.Asn3624Thr | missense_variant | 62/66 | ||
SPTBN5 | XM_017022302.2 | c.8048A>C | p.Asn2683Thr | missense_variant | 50/54 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN5 | ENST00000320955.8 | c.10691A>C | p.Asn3564Thr | missense_variant | 64/68 | 1 | NM_016642.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.869 AC: 131995AN: 151856Hom.: 58072 Cov.: 29
GnomAD3 exomes AF: 0.840 AC: 129704AN: 154454Hom.: 55861 AF XY: 0.845 AC XY: 69138AN XY: 81786
GnomAD4 exome AF: 0.885 AC: 1237319AN: 1398812Hom.: 552871 Cov.: 58 AF XY: 0.885 AC XY: 610305AN XY: 689930
GnomAD4 genome ? AF: 0.869 AC: 132079AN: 151974Hom.: 58109 Cov.: 29 AF XY: 0.867 AC XY: 64364AN XY: 74266
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at