chr3-124973819-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020733.2(HEG1):c.3908G>A(p.Arg1303His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEG1 | ENST00000311127.9 | c.3908G>A | p.Arg1303His | missense_variant | Exon 16 of 17 | 5 | NM_020733.2 | ENSP00000311502.3 | ||
HEG1 | ENST00000650592.2 | c.4208G>A | p.Arg1403His | missense_variant | Exon 17 of 18 | ENSP00000515478.1 | ||||
HEG1 | ENST00000482699.1 | n.89G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 4 | ENSP00000417494.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249226Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135204
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461500Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727058
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3908G>A (p.R1303H) alteration is located in exon 16 (coding exon 16) of the HEG1 gene. This alteration results from a G to A substitution at nucleotide position 3908, causing the arginine (R) at amino acid position 1303 to be replaced by a histidine (H). 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