rs2242944

Variant names:

• chr21-39093252-G-A
• rs2242944

Your query was ambiguous. Multiple possible variants found:

• chr21-39093252-G-A
• chr21-39093252-G-C

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 0.459 in 152,120 control chromosomes in the GnomAD database, including 17,927 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 (17927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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: 0.459 AC: 69742 AN: 152002 Hom.: 17877 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.459 AC: 69860 AN: 152120 Hom.: 17927 Cov.: 33 AF XY: 0.457 AC XY: 33956 AN XY: 74376

African (AFR) AF: 0.704 AC: 29210 AN: 41510

American (AMR) AF: 0.412 AC: 6291 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3460

East Asian (EAS) AF: 0.403 AC: 2086 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2054 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24205 AN: 68002

Other (OTH) AF: 0.450 AC: 947 AN: 2104

Alfa AF: 0.394 Hom.: 49013

Bravo AF: 0.479

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.24
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2242944; hg19: chr21-40465178;