rs1131603
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000355.4(TCN2):c.1127T>C(p.Leu376Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 1,614,044 control chromosomes in the GnomAD database, including 1,756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000355.4 missense
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: 0.0363 AC: 5527AN: 152074Hom.: 137 Cov.: 31
GnomAD3 exomes AF: 0.0422 AC: 10609AN: 251480Hom.: 298 AF XY: 0.0426 AC XY: 5786AN XY: 135914
GnomAD4 exome AF: 0.0444 AC: 64866AN: 1461852Hom.: 1618 Cov.: 31 AF XY: 0.0444 AC XY: 32302AN XY: 727232
GnomAD4 genome AF: 0.0363 AC: 5529AN: 152192Hom.: 138 Cov.: 31 AF XY: 0.0365 AC XY: 2713AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
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This variant is associated with the following publications: (PMID: 28334792, 23754956) -
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
Transcobalamin II deficiency Benign:2
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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