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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.464 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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.471

Alfa AF: 0.408 Hom.: 5970

Bravo AF: 0.471

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2222995; hg19: chr21-40509892;