rs2884681

Variant names:

• chr10-20349137-G-A
• rs2884681

Your query was ambiguous. Multiple possible variants found:

• chr10-20349137-G-A
• chr10-20349137-G-C

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 0.347 in 151,896 control chromosomes in the GnomAD database, including 9,669 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 0.35 (9669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.347 AC: 52703 AN: 151778 Hom.: 9673 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.347 AC: 52709 AN: 151896 Hom.: 9669 Cov.: 31 AF XY: 0.346 AC XY: 25713 AN XY: 74228

African (AFR) AF: 0.218 AC: 9027 AN: 41440

American (AMR) AF: 0.431 AC: 6578 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1126 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2479 AN: 5156

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3768 AN: 10510

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26725 AN: 67938

Other (OTH) AF: 0.365 AC: 771 AN: 2110

Alfa AF: 0.384 Hom.: 6370

Bravo AF: 0.349

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs2884681; hg19: chr10-20638066;