rs2836985

Variant names:

• chr21-39329243-A-G
• rs2836985

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 0.517 in 151,904 control chromosomes in the GnomAD database, including 20,780 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 0.52 (20780 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.517 AC: 78430 AN: 151786 Hom.: 20747 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.517 AC: 78510 AN: 151904 Hom.: 20780 Cov.: 31 AF XY: 0.525 AC XY: 38962 AN XY: 74218

African (AFR) AF: 0.609 AC: 25243 AN: 41432

American (AMR) AF: 0.550 AC: 8375 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1580 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2047 AN: 5170

South Asian (SAS) AF: 0.516 AC: 2484 AN: 4818

European-Finnish (FIN) AF: 0.587 AC: 6177 AN: 10528

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30921 AN: 67946

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.476 Hom.: 9259

Bravo AF: 0.516

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.49
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2836985; hg19: chr21-40701169;