rs225362

Variant names:

• chr21-42317025-A-G
• rs225362

Your query was ambiguous. Multiple possible variants found:

• chr21-42317025-A-G
• chr21-42317025-A-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 0.313 in 152,020 control chromosomes in the GnomAD database, including 9,070 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 0.31 (9070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 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: 0.313 AC: 47610 AN: 151902 Hom.: 9075 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.313 AC: 47605 AN: 152020 Hom.: 9070 Cov.: 31 AF XY: 0.309 AC XY: 22961 AN XY: 74296

African (AFR) AF: 0.121 AC: 5006 AN: 41470

American (AMR) AF: 0.338 AC: 5165 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3464

East Asian (EAS) AF: 0.0177 AC: 91 AN: 5146

South Asian (SAS) AF: 0.338 AC: 1631 AN: 4824

European-Finnish (FIN) AF: 0.378 AC: 3993 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29053 AN: 67958

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.232 Hom.: 647

Bravo AF: 0.301

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs225362; hg19: chr21-43737135; COSMIC: COSV52294231;