rs145351367
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_030962.4(SBF2):c.3819C>T(p.Ser1273Ser) variant causes a synonymous change. The variant allele was found at a frequency of 0.000485 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_030962.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251194Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135812
GnomAD4 exome AF: 0.000504 AC: 737AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.000474 AC XY: 345AN XY: 727234
GnomAD4 genome AF: 0.000302 AC: 46AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:2
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SBF2: BP4, BP7 -
Charcot-Marie-Tooth disease type 4B2 Uncertain: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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Charcot-Marie-Tooth disease Benign:1
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not specified Benign:1
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Charcot-Marie-Tooth disease type 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at