21-30269930-T-A

Variant names:

• chr21-30269930-T-A
• rs10482998

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 0.84 in 151,384 control chromosomes in the GnomAD database, including 53,807 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 0.84 (53807 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.839 AC: 126985 AN: 151264 Hom.: 53742 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.840 AC: 127110 AN: 151384 Hom.: 53807 Cov.: 31 AF XY: 0.839 AC XY: 62095 AN XY: 73984

African (AFR) AF: 0.934 AC: 38097 AN: 40796

American (AMR) AF: 0.838 AC: 12799 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2818 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4430 AN: 5170

South Asian (SAS) AF: 0.883 AC: 4260 AN: 4826

European-Finnish (FIN) AF: 0.752 AC: 7940 AN: 10556

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53981 AN: 67986

Other (OTH) AF: 0.824 AC: 1735 AN: 2106

Alfa AF: 0.820 Hom.: 6012

Bravo AF: 0.848

Asia WGS AF: 0.871 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.53
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs10482998; hg19: chr21-31642248;