14-31304997-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015473.4(HEATR5A):c.5147C>T(p.Thr1716Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015473.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEATR5A | NM_015473.4 | c.5147C>T | p.Thr1716Met | missense_variant | 32/36 | ENST00000543095.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEATR5A | ENST00000543095.7 | c.5147C>T | p.Thr1716Met | missense_variant | 32/36 | 5 | NM_015473.4 | P1 | |
HEATR5A | ENST00000538864.6 | c.4031C>T | p.Thr1344Met | missense_variant | 25/28 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249156Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135164
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727128
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.5147C>T (p.T1716M) alteration is located in exon 32 (coding exon 31) of the HEATR5A gene. This alteration results from a C to T substitution at nucleotide position 5147, causing the threonine (T) at amino acid position 1716 to be replaced by a methionine (M). 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