14-31302494-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015473.4(HEATR5A):c.5265A>G(p.Ile1755Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,582,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEATR5A | NM_015473.4 | c.5265A>G | p.Ile1755Met | missense_variant | 33/36 | ENST00000543095.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEATR5A | ENST00000543095.7 | c.5265A>G | p.Ile1755Met | missense_variant | 33/36 | 5 | NM_015473.4 | P1 | |
ENST00000551799.1 | n.730T>C | non_coding_transcript_exon_variant | 6/6 | 3 | |||||
HEATR5A | ENST00000538864.6 | c.4122+2411A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152062Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000301 AC: 6AN: 199614Hom.: 0 AF XY: 0.0000187 AC XY: 2AN XY: 106712
GnomAD4 exome AF: 0.0000147 AC: 21AN: 1430038Hom.: 0 Cov.: 30 AF XY: 0.00000988 AC XY: 7AN XY: 708250
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152062Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.5265A>G (p.I1755M) alteration is located in exon 33 (coding exon 32) of the HEATR5A gene. This alteration results from a A to G substitution at nucleotide position 5265, causing the isoleucine (I) at amino acid position 1755 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