chrX-53234278-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001111125.3(IQSEC2):c.4408G>A(p.Ala1470Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,026,508 control chromosomes in the GnomAD database, including 76 homozygotes. There are 3,391 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001111125.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00890 AC: 780AN: 87689Hom.: 10 Cov.: 14 AF XY: 0.00736 AC XY: 120AN XY: 16295
GnomAD3 exomes AF: 0.00682 AC: 344AN: 50460Hom.: 2 AF XY: 0.00694 AC XY: 56AN XY: 8070
GnomAD4 exome AF: 0.0123 AC: 11513AN: 938795Hom.: 66 Cov.: 21 AF XY: 0.0121 AC XY: 3271AN XY: 271161
GnomAD4 genome AF: 0.00888 AC: 779AN: 87713Hom.: 10 Cov.: 14 AF XY: 0.00735 AC XY: 120AN XY: 16325
ClinVar
Submissions by phenotype
not provided Benign:5
- -
- -
- -
- -
- -
not specified Benign:4
- -
- -
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. -
- -
Intellectual disability, X-linked 1 Benign:2
- -
- -
Inborn genetic diseases Benign:1
This alteration is classified as 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