rs1187193827
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_017780.4(CHD7):c.2062G>A(p.Ala688Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000393 in 1,525,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_017780.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHD7 | NM_017780.4 | c.2062G>A | p.Ala688Thr | missense_variant | 3/38 | ENST00000423902.7 | NP_060250.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.2062G>A | p.Ala688Thr | missense_variant | 3/38 | 5 | NM_017780.4 | ENSP00000392028 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151594Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 3AN: 148280Hom.: 0 AF XY: 0.0000126 AC XY: 1AN XY: 79630
GnomAD4 exome AF: 0.00000364 AC: 5AN: 1374006Hom.: 0 Cov.: 32 AF XY: 0.00000147 AC XY: 1AN XY: 678670
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151594Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74040
ClinVar
Submissions by phenotype
CHARGE syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at