21-42062474-T-G

Variant names:

• chr21-42062474-T-G
• rs220265

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 0.862 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.909 AC: 37757 AN: 41550

American (AMR) AF: 0.913 AC: 13966 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2977 AN: 3466

East Asian (EAS) AF: 0.590 AC: 3038 AN: 5152

South Asian (SAS) AF: 0.737 AC: 3551 AN: 4820

European-Finnish (FIN) AF: 0.786 AC: 8326 AN: 10588

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58757 AN: 67988

Other (OTH) AF: 0.858 AC: 1814 AN: 2114

Alfa AF: 0.855 Hom.: 24537

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
PhyloP100		0.050
PromoterAI		0.065	Neutral

Splicing

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

Other links and lift over

dbSNP: rs220265; hg19: chr21-43482583;