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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.689

Alfa AF: 0.743 Hom.: 83423

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1191812; hg19: chr2-20224999;