chr5-98856555-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4BP6_ModerateBS2
The NM_001270.4(CHD1):c.4958A>C(p.Lys1653Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K1653E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001270.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD1 | NM_001270.4 | c.4958A>C | p.Lys1653Thr | missense_variant | 36/36 | ENST00000614616.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD1 | ENST00000614616.5 | c.4958A>C | p.Lys1653Thr | missense_variant | 36/36 | 5 | NM_001270.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251204Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135758
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727116
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | CHD1: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at