rs2840837

Variant names:

• chr6-132562444-G-A
• rs2840837

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 0.345 in 119,186 control chromosomes in the GnomAD database, including 6,156 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 0.34 (6156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.345 AC: 41064 AN: 119082 Hom.: 6160 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.267

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.345 AC: 41077 AN: 119186 Hom.: 6156 Cov.: 31 AF XY: 0.346 AC XY: 20090 AN XY: 58070

African (AFR) AF: 0.236 AC: 7875 AN: 33312

American (AMR) AF: 0.373 AC: 4686 AN: 12560

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1014 AN: 2712

East Asian (EAS) AF: 0.184 AC: 267 AN: 1448

South Asian (SAS) AF: 0.323 AC: 1056 AN: 3272

European-Finnish (FIN) AF: 0.474 AC: 4225 AN: 8916

Middle Eastern (MID) AF: 0.261 AC: 58 AN: 222

European-Non Finnish (NFE) AF: 0.388 AC: 21098 AN: 54354

Other (OTH) AF: 0.346 AC: 555 AN: 1602

Alfa AF: 0.295 Hom.: 11599

Bravo AF: 0.260

Asia WGS AF: 0.130 AC: 445 AN: 3390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2840837; hg19: chr6-132883583;