rs2094871

Variant names:

• chr21-39088933-G-A
• rs2094871

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 0.348 in 152,144 control chromosomes in the GnomAD database, including 9,445 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 0.35 (9445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 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: 0.348 AC: 52937 AN: 152026 Hom.: 9424 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.348 AC: 52998 AN: 152144 Hom.: 9445 Cov.: 33 AF XY: 0.348 AC XY: 25902 AN XY: 74388

African (AFR) AF: 0.375 AC: 15576 AN: 41522

American (AMR) AF: 0.366 AC: 5586 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2054 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4820

European-Finnish (FIN) AF: 0.258 AC: 2729 AN: 10590

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22594 AN: 67982

Other (OTH) AF: 0.361 AC: 761 AN: 2108

Alfa AF: 0.342 Hom.: 1104

Bravo AF: 0.359

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2094871; hg19: chr21-40460859;