rs76802001
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000355.4(TCN2):c.1023G>A(p.Pro341Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0312 in 1,614,028 control chromosomes in the GnomAD database, including 957 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000355.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0246 AC: 3743AN: 152040Hom.: 65 Cov.: 31
GnomAD3 exomes AF: 0.0253 AC: 6366AN: 251470Hom.: 123 AF XY: 0.0255 AC XY: 3466AN XY: 135914
GnomAD4 exome AF: 0.0319 AC: 46561AN: 1461870Hom.: 892 Cov.: 32 AF XY: 0.0313 AC XY: 22735AN XY: 727240
GnomAD4 genome AF: 0.0246 AC: 3744AN: 152158Hom.: 65 Cov.: 31 AF XY: 0.0238 AC XY: 1771AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:2
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Transcobalamin II deficiency Benign:2
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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at