1-31790712-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_144569.7(SPOCD1):c.3542G>A(p.Arg1181His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,551,774 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_144569.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000198 AC: 31AN: 156288Hom.: 1 AF XY: 0.000206 AC XY: 17AN XY: 82386
GnomAD4 exome AF: 0.000104 AC: 145AN: 1399590Hom.: 1 Cov.: 31 AF XY: 0.000110 AC XY: 76AN XY: 690344
GnomAD4 genome AF: 0.000112 AC: 17AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:1
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