rs2827107

chr21-21881735-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 0.275 in 151,978 control chromosomes in the GnomAD database, including 6,186 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 0.28 (6186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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: 0.275 AC: 41822 AN: 151858 Hom.: 6192 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.275 AC: 41847 AN: 151978 Hom.: 6186 Cov.: 32 AF XY: 0.279 AC XY: 20744 AN XY: 74306

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.275

Alfa AF: 0.247 Hom.: 6419

Bravo AF: 0.281

Asia WGS AF: 0.449 AC: 1553 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2827107; hg19: chr21-23254055;