7-27100878-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006735.4(HOXA2):c.979G>A(p.Val327Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00095 in 1,614,204 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 Uncertain significance (★).
Frequency
Consequence
NM_006735.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000874 AC: 133AN: 152194Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000930 AC: 234AN: 251490Hom.: 2 AF XY: 0.000971 AC XY: 132AN XY: 135918
GnomAD4 exome AF: 0.000958 AC: 1400AN: 1461892Hom.: 1 Cov.: 32 AF XY: 0.000969 AC XY: 705AN XY: 727246
GnomAD4 genome AF: 0.000873 AC: 133AN: 152312Hom.: 1 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74476
ClinVar
Submissions by phenotype
Bilateral microtia-deafness-cleft palate syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at