chr3-124977881-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020733.2(HEG1):c.3799G>A(p.Ala1267Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000144 in 1,575,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020733.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEG1 | ENST00000311127.9 | c.3799G>A | p.Ala1267Thr | missense_variant | Exon 15 of 17 | 5 | NM_020733.2 | ENSP00000311502.3 | ||
HEG1 | ENST00000650592.2 | c.4099G>A | p.Ala1367Thr | missense_variant | Exon 16 of 18 | ENSP00000515478.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 20AN: 193734Hom.: 0 AF XY: 0.0000773 AC XY: 8AN XY: 103444
GnomAD4 exome AF: 0.000154 AC: 219AN: 1423200Hom.: 0 Cov.: 29 AF XY: 0.000153 AC XY: 108AN XY: 704274
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3799G>A (p.A1267T) alteration is located in exon 15 (coding exon 15) of the HEG1 gene. This alteration results from a G to A substitution at nucleotide position 3799, causing the alanine (A) at amino acid position 1267 to be replaced by a threonine (T). 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