rs2222995

Variant names:

• chr21-39137966-G-A
• rs2222995

Your query was ambiguous. Multiple possible variants found:

• chr21-39137966-G-A
• chr21-39137966-G-T

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 0.464 in 151,874 control chromosomes in the GnomAD database, including 16,670 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 0.46 (16670 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70372 AN: 151756 Hom.: 16652 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.464 AC: 70426 AN: 151874 Hom.: 16670 Cov.: 31 AF XY: 0.469 AC XY: 34853 AN XY: 74244

African (AFR) AF: 0.540 AC: 22326 AN: 41374

American (AMR) AF: 0.525 AC: 8014 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3437 AN: 5166

South Asian (SAS) AF: 0.488 AC: 2349 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5133 AN: 10536

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26479 AN: 67944

Other (OTH) AF: 0.471 AC: 989 AN: 2098

Alfa AF: 0.407 Hom.: 6578

Bravo AF: 0.471

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.011
DANN	Benign	0.57
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2222995; hg19: chr21-40509892;