chr7-27100851-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006735.4(HOXA2):c.1006C>A(p.Leu336Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,614,258 control chromosomes in the GnomAD database, including 1 homozygotes. 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. L336V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006735.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXA2 | NM_006735.4 | c.1006C>A | p.Leu336Ile | missense_variant | 2/2 | ENST00000222718.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXA2 | ENST00000222718.7 | c.1006C>A | p.Leu336Ile | missense_variant | 2/2 | 1 | NM_006735.4 | P1 | |
HOXA2 | ENST00000612779.1 | n.1836C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.000723 AC: 110AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251494Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135922
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461894Hom.: 1 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 727248
GnomAD4 genome ? AF: 0.000715 AC: 109AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.000711 AC XY: 53AN XY: 74510
ClinVar
Submissions by phenotype
HOXA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 31, 2024 | 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