chrX-17727892-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001291867.2(NHS):c.3786G>A(p.Thr1262Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,209,961 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 77 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001291867.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000716 AC: 8AN: 111723Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33921
GnomAD3 exomes AF: 0.0000818 AC: 15AN: 183421Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67865
GnomAD4 exome AF: 0.000222 AC: 244AN: 1098238Hom.: 0 Cov.: 33 AF XY: 0.000209 AC XY: 76AN XY: 363592
GnomAD4 genome AF: 0.0000716 AC: 8AN: 111723Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33921
ClinVar
Submissions by phenotype
not specified Benign:1
- -
Nance-Horan syndrome Benign:1
- -
NHS-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at