chr14-31293424-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015473.4(HEATR5A):c.6022C>T(p.Arg2008Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R2008H) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEATR5A | NM_015473.4 | c.6022C>T | p.Arg2008Cys | missense_variant | 36/36 | ENST00000543095.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEATR5A | ENST00000543095.7 | c.6022C>T | p.Arg2008Cys | missense_variant | 36/36 | 5 | NM_015473.4 | P1 | |
ENST00000551799.1 | n.401-2008G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
HEATR5A | ENST00000538864.6 | c.4681C>T | p.Arg1561Cys | missense_variant | 28/28 | 5 | |||
HEATR5A | ENST00000551414.1 | n.2215C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249170Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135170
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461564Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727070
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.6022C>T (p.R2008C) alteration is located in exon 36 (coding exon 35) of the HEATR5A gene. This alteration results from a C to T substitution at nucleotide position 6022, causing the arginine (R) at amino acid position 2008 to be replaced by a cysteine (C). 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