rs8164
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000543.5(SMPD1):c.*45G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,531,524 control chromosomes in the GnomAD database, including 16,955 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000543.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.166 AC: 25286AN: 152168Hom.: 2493 Cov.: 33
GnomAD3 exomes AF: 0.131 AC: 28896AN: 220964Hom.: 2263 AF XY: 0.133 AC XY: 16270AN XY: 122172
GnomAD4 exome AF: 0.139 AC: 191808AN: 1379238Hom.: 14454 Cov.: 22 AF XY: 0.140 AC XY: 96671AN XY: 689874
GnomAD4 genome AF: 0.166 AC: 25320AN: 152286Hom.: 2501 Cov.: 33 AF XY: 0.163 AC XY: 12174AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
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Niemann-Pick disease, type A Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at