21-42062052-G-A

Position:

• chr21-42062052-G-A

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 0.509 in 151,984 control chromosomes in the GnomAD database, including 20,374 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 0.51 (20374 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42062052G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77369 AN: 151866 Hom.: 20366 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.509 AC: 77405 AN: 151984 Hom.: 20374 Cov.: 32 AF XY: 0.505 AC XY: 37480 AN XY: 74274

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.521

Alfa AF: 0.525 Hom.: 2052

Bravo AF: 0.529

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
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: rs220263; hg19: chr21-43482161;