rs2882969

Positions:

• chr2-203781465-G-C

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 0.679 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.676

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882969; hg19: chr2-204646188;