14-31302429-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.5330C>T(p.Ser1777Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000945 in 1,598,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/16 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.5330C>T | p.Ser1777Leu | missense_variant | 33/36 | ENST00000543095.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEATR5A | ENST00000543095.7 | c.5330C>T | p.Ser1777Leu | missense_variant | 33/36 | 5 | NM_015473.4 | P1 | |
ENST00000551799.1 | n.665G>A | non_coding_transcript_exon_variant | 6/6 | 3 | |||||
HEATR5A | ENST00000538864.6 | c.4122+2476C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151942Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000134 AC: 30AN: 223228Hom.: 0 AF XY: 0.000133 AC XY: 16AN XY: 120378
GnomAD4 exome AF: 0.0000926 AC: 134AN: 1446342Hom.: 0 Cov.: 30 AF XY: 0.0000989 AC XY: 71AN XY: 717826
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152060Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.5330C>T (p.S1777L) alteration is located in exon 33 (coding exon 32) of the HEATR5A gene. This alteration results from a C to T substitution at nucleotide position 5330, causing the serine (S) at amino acid position 1777 to be replaced by a leucine (L). 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