rs2836878

Variant names:

• chr21-39093608-G-A
• rs2836878

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 0.229 in 152,216 control chromosomes in the GnomAD database, including 4,323 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 0.23 (4323 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 107 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 (AMR) allele frequency at 95% confidence interval = 0.28 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: 0.229 AC: 34774 AN: 152098 Hom.: 4309 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.229 AC: 34814 AN: 152216 Hom.: 4323 Cov.: 33 AF XY: 0.229 AC XY: 17067 AN XY: 74426

African (AFR) AF: 0.139 AC: 5772 AN: 41536

American (AMR) AF: 0.287 AC: 4390 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.170 AC: 876 AN: 5168

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4832

European-Finnish (FIN) AF: 0.230 AC: 2436 AN: 10592

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18365 AN: 68012

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.262 Hom.: 24565

Bravo AF: 0.232

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2836878; hg19: chr21-40465534;