chr3-11260082-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001098212.2(HRH1):c.1045G>C(p.Asp349His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 1,614,128 control chromosomes in the GnomAD database, including 9 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001098212.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRH1 | NM_001098212.2 | c.1045G>C | p.Asp349His | missense_variant | 2/2 | ENST00000431010.3 | |
HRH1 | NM_000861.3 | c.1045G>C | p.Asp349His | missense_variant | 3/3 | ||
HRH1 | NM_001098211.2 | c.1045G>C | p.Asp349His | missense_variant | 2/2 | ||
HRH1 | NM_001098213.2 | c.1045G>C | p.Asp349His | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRH1 | ENST00000431010.3 | c.1045G>C | p.Asp349His | missense_variant | 2/2 | 1 | NM_001098212.2 | P1 | |
HRH1 | ENST00000397056.1 | c.1045G>C | p.Asp349His | missense_variant | 3/3 | 1 | P1 | ||
HRH1 | ENST00000438284.2 | c.1045G>C | p.Asp349His | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000861 AC: 131AN: 152134Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00171 AC: 430AN: 251326Hom.: 5 AF XY: 0.00157 AC XY: 213AN XY: 135838
GnomAD4 exome AF: 0.000456 AC: 666AN: 1461876Hom.: 8 Cov.: 34 AF XY: 0.000429 AC XY: 312AN XY: 727238
GnomAD4 genome ? AF: 0.000860 AC: 131AN: 152252Hom.: 1 Cov.: 32 AF XY: 0.000981 AC XY: 73AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at