rs2827980

Variant names:

• chr21-23230664-A-G
• rs2827980

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 0.114 in 151,844 control chromosomes in the GnomAD database, including 1,032 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 0.11 (1032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.17 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: 0.114 AC: 17358 AN: 151726 Hom.: 1031 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0635

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.114 AC: 17368 AN: 151844 Hom.: 1032 Cov.: 32 AF XY: 0.115 AC XY: 8563 AN XY: 74192

African (AFR) AF: 0.102 AC: 4230 AN: 41510

American (AMR) AF: 0.0861 AC: 1309 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0635 AC: 220 AN: 3462

East Asian (EAS) AF: 0.138 AC: 710 AN: 5146

South Asian (SAS) AF: 0.180 AC: 869 AN: 4818

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8595 AN: 67800

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.120 Hom.: 1323

Bravo AF: 0.109

Asia WGS AF: 0.146 AC: 507 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.22
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2827980; hg19: chr21-24602986;