rs2827732

Variant names:

• chr21-22813646-C-A
• rs2827732

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 0.196 in 151,864 control chromosomes in the GnomAD database, including 3,173 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 0.20 (3173 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.196 AC: 29754 AN: 151746 Hom.: 3160 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29810 AN: 151864 Hom.: 3173 Cov.: 33 AF XY: 0.198 AC XY: 14716 AN XY: 74246

African (AFR) AF: 0.267 AC: 11040 AN: 41282

American (AMR) AF: 0.203 AC: 3103 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.0879 AC: 455 AN: 5174

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1855 AN: 10580

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11243 AN: 67956

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.176 Hom.: 1884

Bravo AF: 0.201

Asia WGS AF: 0.174 AC: 608 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2827732; hg19: chr21-24185967;