chr2-215347616-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1
The NM_004044.7(ATIC):c.1503+675T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 490,610 control chromosomes in the GnomAD database, including 27,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).
Frequency
Consequence
NM_004044.7 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.266 AC: 40398AN: 151642Hom.: 6092 Cov.: 31
GnomAD3 exomes AF: 0.340 AC: 47119AN: 138606Hom.: 8478 AF XY: 0.353 AC XY: 26451AN XY: 74924
GnomAD4 exome AF: 0.343 AC: 116330AN: 338850Hom.: 21063 Cov.: 0 AF XY: 0.357 AC XY: 67511AN XY: 189216
GnomAD4 genome AF: 0.266 AC: 40429AN: 151760Hom.: 6101 Cov.: 31 AF XY: 0.266 AC XY: 19740AN XY: 74138
ClinVar
Submissions by phenotype
not provided Benign:1
- -
methotrexate response - Efficacy Other:1
PharmGKB Level of Evidence 2B: Variants in Level 2B clinical annotations are not in PharmGKB’s Tier 1 VIPs. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2B clinical annotations must be supported by at least two independent publications. Drug-variant association: Efficacy
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at