chr14-21385739-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001170629.2(CHD8):c.7620C>T(p.Asp2540Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00064 in 1,551,282 control chromosomes in the GnomAD database, including 2 homozygotes. 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_001170629.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHD8 | NM_001170629.2 | c.7620C>T | p.Asp2540Asp | synonymous_variant | Exon 38 of 38 | ENST00000646647.2 | NP_001164100.1 | |
CHD8 | NM_020920.4 | c.6783C>T | p.Asp2261Asp | synonymous_variant | Exon 38 of 38 | NP_065971.2 | ||
LOC107984643 | XR_001750627.2 | n.441+1026G>A | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000521 AC: 79AN: 151618Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000895 AC: 141AN: 157494Hom.: 0 AF XY: 0.000950 AC XY: 79AN XY: 83158
GnomAD4 exome AF: 0.000653 AC: 914AN: 1399550Hom.: 2 Cov.: 35 AF XY: 0.000663 AC XY: 458AN XY: 690284
GnomAD4 genome AF: 0.000521 AC: 79AN: 151732Hom.: 0 Cov.: 30 AF XY: 0.000526 AC XY: 39AN XY: 74144
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
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CHD8: BS1, BS2 -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at