chr1-247451382-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001004492.2(OR2B11):c.601A>G(p.Thr201Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 1,614,068 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001004492.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR2B11 | NM_001004492.2 | c.601A>G | p.Thr201Ala | missense_variant | 2/2 | ENST00000641149.2 | |
OR2B11 | NR_169840.1 | n.1255A>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2B11 | ENST00000641149.2 | c.601A>G | p.Thr201Ala | missense_variant | 2/2 | NM_001004492.2 | P1 | ||
OR2B11 | ENST00000641527.1 | c.601A>G | p.Thr201Ala | missense_variant | 3/3 | P1 | |||
OR2B11 | ENST00000641613.1 | n.1255A>G | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251354Hom.: 1 AF XY: 0.000243 AC XY: 33AN XY: 135870
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461878Hom.: 2 Cov.: 60 AF XY: 0.000121 AC XY: 88AN XY: 727238
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at