chr21-42062474-T-G

Variant names:

• chr21-42062474-T-G
• rs220265

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 0.862 in 152,188 control chromosomes in the GnomAD database, including 56,820 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 0.86 (56820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.901 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: 0.862 AC: 131060 AN: 152070 Hom.: 56771 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.862 AC: 131168 AN: 152188 Hom.: 56820 Cov.: 32 AF XY: 0.857 AC XY: 63766 AN XY: 74388

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.858

Alfa AF: 0.804 Hom.: 830

Bravo AF: 0.875

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs220265; hg19: chr21-43482583;