rs735421
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000742.4(CHRNA2):c.1465-21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,550 control chromosomes in the GnomAD database, including 80,319 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000742.4 intron
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: 0.272 AC: 41334AN: 152086Hom.: 6429 Cov.: 33
GnomAD3 exomes AF: 0.310 AC: 77683AN: 250436Hom.: 12662 AF XY: 0.310 AC XY: 41992AN XY: 135454
GnomAD4 exome AF: 0.315 AC: 459696AN: 1461346Hom.: 73884 Cov.: 35 AF XY: 0.314 AC XY: 228139AN XY: 726984
GnomAD4 genome AF: 0.272 AC: 41357AN: 152204Hom.: 6435 Cov.: 33 AF XY: 0.274 AC XY: 20412AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 62% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 58. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at