rs2882969

Variant names:

• chr2-203781465-G-C
• rs2882969

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 0.679 in 152,002 control chromosomes in the GnomAD database, including 35,572 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 0.68 (35572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.821 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: 0.679 AC: 103112 AN: 151882 Hom.: 35567 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.679 AC: 103156 AN: 152002 Hom.: 35572 Cov.: 31 AF XY: 0.682 AC XY: 50722 AN XY: 74318

African (AFR) AF: 0.577 AC: 23873 AN: 41404

American (AMR) AF: 0.721 AC: 11012 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5166

South Asian (SAS) AF: 0.843 AC: 4065 AN: 4822

European-Finnish (FIN) AF: 0.781 AC: 8266 AN: 10578

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48850 AN: 67972

Other (OTH) AF: 0.676 AC: 1427 AN: 2110

Alfa AF: 0.700 Hom.: 4674

Bravo AF: 0.666

Asia WGS AF: 0.696 AC: 2418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.61
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2882969; hg19: chr2-204646188;