chr14-31293423-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015473.4(HEATR5A):c.6023G>A(p.Arg2008His) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,613,774 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2008C) has been classified as Uncertain significance.
Frequency
Consequence
NM_015473.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEATR5A | NM_015473.4 | c.6023G>A | p.Arg2008His | missense_variant | 36/36 | ENST00000543095.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEATR5A | ENST00000543095.7 | c.6023G>A | p.Arg2008His | missense_variant | 36/36 | 5 | NM_015473.4 | P1 | |
ENST00000551799.1 | n.401-2009C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
HEATR5A | ENST00000538864.6 | c.4682G>A | p.Arg1561His | missense_variant | 28/28 | 5 | |||
HEATR5A | ENST00000551414.1 | n.2216G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 249168Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135168
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461600Hom.: 1 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727080
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2021 | The c.6023G>A (p.R2008H) alteration is located in exon 36 (coding exon 35) of the HEATR5A gene. This alteration results from a G to A substitution at nucleotide position 6023, causing the arginine (R) at amino acid position 2008 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at