chr1-248638846-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001001827.2(OR2T35):c.413G>A(p.Arg138His) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001827.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 43178Hom.: 0 Cov.: 6 FAILED QC
GnomAD3 exomes AF: 0.0000368 AC: 3AN: 81532Hom.: 0 AF XY: 0.0000713 AC XY: 3AN XY: 42092
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000454 AC: 32AN: 704762Hom.: 0 Cov.: 9 AF XY: 0.0000487 AC XY: 18AN XY: 369900
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 43178Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 20474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.413G>A (p.R138H) alteration is located in exon 1 (coding exon 1) of the OR2T35 gene. This alteration results from a G to A substitution at nucleotide position 413, causing the arginine (R) at amino acid position 138 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