rs2836889

Variant names:

• chr21-39113648-C-T
• rs2836889

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 0.331 in 151,950 control chromosomes in the GnomAD database, including 8,749 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 0.33 (8749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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: 0.331 AC: 50331 AN: 151832 Hom.: 8732 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.331 AC: 50371 AN: 151950 Hom.: 8749 Cov.: 32 AF XY: 0.334 AC XY: 24811 AN XY: 74254

African (AFR) AF: 0.238 AC: 9847 AN: 41422

American (AMR) AF: 0.436 AC: 6663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1192 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5176

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4820

European-Finnish (FIN) AF: 0.411 AC: 4335 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24646 AN: 67924

Other (OTH) AF: 0.333 AC: 700 AN: 2104

Alfa AF: 0.353 Hom.: 40625

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2836889; hg19: chr21-40485574;