rs10482998

Variant names:

• chr21-30269930-T-A
• rs10482998

Your query was ambiguous. Multiple possible variants found:

• chr21-30269930-T-A
• chr21-30269930-T-C

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 0.84 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.824

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482998; hg19: chr21-31642248;