NM_001271.4:c.693-20C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001271.4(CHD2):c.693-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00469 in 1,609,170 control chromosomes in the GnomAD database, including 444 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001271.4 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: 0.00803 AC: 1222AN: 152098Hom.: 55 Cov.: 32
GnomAD3 exomes AF: 0.0174 AC: 4333AN: 248624Hom.: 281 AF XY: 0.0131 AC XY: 1763AN XY: 134510
GnomAD4 exome AF: 0.00434 AC: 6330AN: 1456954Hom.: 388 Cov.: 29 AF XY: 0.00381 AC XY: 2762AN XY: 724950
GnomAD4 genome AF: 0.00803 AC: 1223AN: 152216Hom.: 56 Cov.: 32 AF XY: 0.00894 AC XY: 665AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:3
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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This variant is classified as Benign based on local population frequency. This variant was detected in 30% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 28. Only high quality variants are reported. -
not provided Benign:1
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Developmental and epileptic encephalopathy 94 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at