chr7-27199919-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000522.5(HOXA13):c.159C>T(p.Ala53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000284 in 1,056,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A53A) has been classified as Likely benign.
Frequency
Consequence
NM_000522.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXA13 | NM_000522.5 | c.159C>T | p.Ala53= | synonymous_variant | 1/2 | ENST00000649031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXA13 | ENST00000649031.1 | c.159C>T | p.Ala53= | synonymous_variant | 1/2 | NM_000522.5 | P1 | ||
HOTTIP | ENST00000421733.1 | n.168-704G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
HOTTIP | ENST00000605136.6 | n.86+589G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000284 AC: 3AN: 1056630Hom.: 0 Cov.: 20 AF XY: 0.00000393 AC XY: 2AN XY: 508646
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at