rs2827732

Positions:

• chr21-22813646-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0879

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.199

Alfa AF: 0.175 Hom.: 1524

Bravo AF: 0.201

Asia WGS AF: 0.174 AC: 608 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2827732; hg19: chr21-24185967;