rs1191812

Variant names:

• chr2-20025238-A-C
• rs1191812

Your query was ambiguous. Multiple possible variants found:

• chr2-20025238-A-C
• chr2-20025238-A-G
• chr2-20025238-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.645 in 152,076 control chromosomes in the GnomAD database, including 33,256 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (33256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.859
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98102 AN: 151956 Hom.: 33255 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.690

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.645 AC: 98134 AN: 152076 Hom.: 33256 Cov.: 32 AF XY: 0.643 AC XY: 47763 AN XY: 74338

African (AFR) AF: 0.429 AC: 17796 AN: 41486

American (AMR) AF: 0.676 AC: 10337 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2751 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3027 AN: 5150

South Asian (SAS) AF: 0.754 AC: 3630 AN: 4816

European-Finnish (FIN) AF: 0.655 AC: 6923 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51353 AN: 67986

Other (OTH) AF: 0.689 AC: 1451 AN: 2106

Alfa AF: 0.719 Hom.: 132597

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.74
PhyloP100		0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1191812; hg19: chr2-20224999;