12-12987176-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015987.5(HEBP1):c.374G>A(p.Arg125Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R125W) has been classified as Uncertain significance.
Frequency
Consequence
NM_015987.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEBP1 | NM_015987.5 | c.374G>A | p.Arg125Gln | missense_variant | Exon 3 of 4 | ENST00000014930.9 | NP_057071.2 | |
GPRC5D-AS1 | NR_149067.1 | n.177+7554C>T | intron_variant | Intron 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEBP1 | ENST00000014930.9 | c.374G>A | p.Arg125Gln | missense_variant | Exon 3 of 4 | 1 | NM_015987.5 | ENSP00000014930.4 | ||
HEBP1 | ENST00000647702.1 | c.428G>A | p.Arg143Gln | missense_variant | Exon 3 of 4 | ENSP00000496930.1 | ||||
HEBP1 | ENST00000536942.1 | c.374G>A | p.Arg125Gln | missense_variant | Exon 3 of 3 | 2 | ENSP00000441678.1 | |||
HEBP1 | ENST00000535636.1 | c.161G>A | p.Arg54Gln | missense_variant | Exon 2 of 3 | 5 | ENSP00000442020.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251276Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135798
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461722Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727156
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.374G>A (p.R125Q) alteration is located in exon 3 (coding exon 3) of the HEBP1 gene. This alteration results from a G to A substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a glutamine (Q). 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