21-42060002-G-C

Variant names:

• chr21-42060002-G-C
• rs220260

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 0.786 in 152,198 control chromosomes in the GnomAD database, including 47,948 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 0.79 (47948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119493 AN: 152080 Hom.: 47892 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.786 AC: 119607 AN: 152198 Hom.: 47948 Cov.: 33 AF XY: 0.780 AC XY: 58015 AN XY: 74396

African (AFR) AF: 0.902 AC: 37466 AN: 41556

American (AMR) AF: 0.800 AC: 12231 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2779 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1768 AN: 5164

South Asian (SAS) AF: 0.617 AC: 2979 AN: 4828

European-Finnish (FIN) AF: 0.731 AC: 7738 AN: 10584

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52197 AN: 67980

Other (OTH) AF: 0.773 AC: 1632 AN: 2112

Alfa AF: 0.785 Hom.: 5854

Bravo AF: 0.797

Asia WGS AF: 0.497 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.51
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs220260; hg19: chr21-43480111;