7-27173609-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018951.4(HOXA10):c.698C>T(p.Ala233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00184 in 1,531,588 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A233A) has been classified as Benign.
Frequency
Consequence
NM_018951.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXA10 | NM_018951.4 | c.698C>T | p.Ala233Val | missense_variant | 1/2 | ENST00000283921.5 | |
HOXA10-HOXA9 | NR_037940.1 | n.616+6037C>T | intron_variant, non_coding_transcript_variant | ||||
HOXA10 | NR_037939.2 | n.217-1436C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXA10 | ENST00000283921.5 | c.698C>T | p.Ala233Val | missense_variant | 1/2 | 1 | NM_018951.4 | P2 | |
HOXA10 | ENST00000396344.4 | c.11-1436C>T | intron_variant | 1 | A1 | ||||
HOXA9 | ENST00000465941.1 | n.479+1093C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 183AN: 151914Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000887 AC: 110AN: 124008Hom.: 0 AF XY: 0.000809 AC XY: 55AN XY: 68018
GnomAD4 exome AF: 0.00191 AC: 2640AN: 1379568Hom.: 2 Cov.: 33 AF XY: 0.00179 AC XY: 1219AN XY: 680142
GnomAD4 genome AF: 0.00120 AC: 183AN: 152020Hom.: 0 Cov.: 33 AF XY: 0.00120 AC XY: 89AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at