NM_001271.4:c.3573G>A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001271.4(CHD2):c.3573G>A(p.Gln1191Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 1,613,930 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 Likely benign (★★).
Frequency
Consequence
NM_001271.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.3573G>A | p.Gln1191Gln | synonymous_variant | Exon 28 of 39 | 5 | NM_001271.4 | ENSP00000377747.4 | ||
CHD2 | ENST00000637789.1 | n.*148G>A | non_coding_transcript_exon_variant | Exon 5 of 9 | 5 | ENSP00000489767.1 | ||||
CHD2 | ENST00000637789.1 | n.*148G>A | 3_prime_UTR_variant | Exon 5 of 9 | 5 | ENSP00000489767.1 |
Frequencies
GnomAD3 genomes AF: 0.00253 AC: 385AN: 152236Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000667 AC: 167AN: 250504Hom.: 0 AF XY: 0.000458 AC XY: 62AN XY: 135456
GnomAD4 exome AF: 0.000259 AC: 378AN: 1461576Hom.: 0 Cov.: 31 AF XY: 0.000227 AC XY: 165AN XY: 727094
GnomAD4 genome AF: 0.00253 AC: 386AN: 152354Hom.: 2 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
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. -
not provided Benign:1
- -
Developmental and epileptic encephalopathy 94 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at