rs2827980

Positions:

• chr21-23230664-A-G

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 0.114 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.23230664A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0635

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.105

Alfa AF: 0.122 Hom.: 1056

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2827980; hg19: chr21-24602986;