rs2836805

Variant names:

• chr21-38982518-C-T
• rs2836805

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 0.257 in 151,984 control chromosomes in the GnomAD database, including 5,253 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 0.26 (5253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 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: 0.257 AC: 39096 AN: 151866 Hom.: 5251 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.257 AC: 39118 AN: 151984 Hom.: 5253 Cov.: 32 AF XY: 0.252 AC XY: 18746 AN XY: 74288

African (AFR) AF: 0.216 AC: 8945 AN: 41416

American (AMR) AF: 0.222 AC: 3389 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5178

South Asian (SAS) AF: 0.185 AC: 891 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2502 AN: 10538

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20468 AN: 67972

Other (OTH) AF: 0.259 AC: 546 AN: 2112

Alfa AF: 0.281 Hom.: 12007

Bravo AF: 0.256

Asia WGS AF: 0.169 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2836805; hg19: chr21-40354444;