rs1869051

Variant names:

• chr2-133686449-G-A
• rs1869051

Your query was ambiguous. Multiple possible variants found:

• chr2-133686449-G-A
• chr2-133686449-G-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 0.644 in 152,002 control chromosomes in the GnomAD database, including 31,931 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 0.64 (31931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.644 AC: 97835 AN: 151884 Hom.: 31870 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.644 AC: 97956 AN: 152002 Hom.: 31931 Cov.: 32 AF XY: 0.644 AC XY: 47838 AN XY: 74288

African (AFR) AF: 0.708 AC: 29353 AN: 41484

American (AMR) AF: 0.606 AC: 9250 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2179 AN: 3464

East Asian (EAS) AF: 0.749 AC: 3853 AN: 5144

South Asian (SAS) AF: 0.609 AC: 2932 AN: 4816

European-Finnish (FIN) AF: 0.627 AC: 6632 AN: 10570

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41781 AN: 67948

Other (OTH) AF: 0.644 AC: 1357 AN: 2108

Alfa AF: 0.623 Hom.: 20348

Bravo AF: 0.648

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1869051; hg19: chr2-134444020; COSMIC: COSV65107417;