chr1-31623551-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001525.3(HCRTR1):c.767G>A(p.Arg256Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,613,304 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R256W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001525.3 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 |
---|---|---|---|---|---|---|---|
HCRTR1 | NM_001525.3 | c.767G>A | p.Arg256Gln | missense_variant | 7/9 | ENST00000403528.7 | |
HCRTR1 | XM_024446605.2 | c.767G>A | p.Arg256Gln | missense_variant | 8/11 | ||
HCRTR1 | XM_017001107.2 | c.767G>A | p.Arg256Gln | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCRTR1 | ENST00000403528.7 | c.767G>A | p.Arg256Gln | missense_variant | 7/9 | 5 | NM_001525.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000484 AC: 12AN: 247972Hom.: 0 AF XY: 0.0000669 AC XY: 9AN XY: 134602
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1460988Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 726800
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.767G>A (p.R256Q) alteration is located in exon 7 (coding exon 5) of the HCRTR1 gene. This alteration results from a G to A substitution at nucleotide position 767, causing the arginine (R) at amino acid position 256 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