chr8-142741814-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP4_StrongBS1_SupportingBS2
The NM_020427.3(SLURP1):c.167C>T(p.Thr56Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000303 in 1,612,142 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020427.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLURP1 | NM_020427.3 | c.167C>T | p.Thr56Met | missense_variant | 2/3 | ENST00000246515.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLURP1 | ENST00000246515.2 | c.167C>T | p.Thr56Met | missense_variant | 2/3 | 1 | NM_020427.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000627 AC: 156AN: 248974Hom.: 2 AF XY: 0.000896 AC XY: 121AN XY: 135054
GnomAD4 exome AF: 0.000323 AC: 472AN: 1459820Hom.: 4 Cov.: 32 AF XY: 0.000493 AC XY: 358AN XY: 726250
GnomAD4 genome AF: 0.000112 AC: 17AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74478
ClinVar
Submissions by phenotype
Acroerythrokeratoderma Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at