rs10482891

chr21-17891674-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 0.0786 in 152,112 control chromosomes in the GnomAD database, including 1,210 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 0.079 (1210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11913 AN: 151994 Hom.: 1204 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.00920

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0786 AC: 11957 AN: 152112 Hom.: 1210 Cov.: 31 AF XY: 0.0769 AC XY: 5719 AN XY: 74394

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0701

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00918

Gnomad4 OTH AF: 0.0784

Alfa AF: 0.0400 Hom.: 134

Bravo AF: 0.0880

Asia WGS AF: 0.0620 AC: 217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.15
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482891; hg19: chr21-19263991;