6-139135551-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016217.3(HECA):c.155C>T(p.Ala52Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 961,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016217.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECA | NM_016217.3 | c.155C>T | p.Ala52Val | missense_variant | 1/4 | ENST00000367658.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECA | ENST00000367658.3 | c.155C>T | p.Ala52Val | missense_variant | 1/4 | 1 | NM_016217.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000974 AC: 14AN: 143762Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.000127 AC: 104AN: 818214Hom.: 0 Cov.: 28 AF XY: 0.000132 AC XY: 50AN XY: 378094
GnomAD4 genome AF: 0.0000974 AC: 14AN: 143762Hom.: 0 Cov.: 30 AF XY: 0.0000859 AC XY: 6AN XY: 69850
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | The c.155C>T (p.A52V) alteration is located in exon 1 (coding exon 1) of the HECA gene. This alteration results from a C to T substitution at nucleotide position 155, causing the alanine (A) at amino acid position 52 to be replaced by a valine (V). 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