rs10483084

Variant names:

• chr21-41975215-G-A
• rs10483084

Your query was ambiguous. Multiple possible variants found:

• chr21-41975215-G-A
• chr21-41975215-G-C

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 0.232 in 152,146 control chromosomes in the GnomAD database, including 4,582 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 0.23 (4582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.232 AC: 35292 AN: 152028 Hom.: 4579 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.232 AC: 35317 AN: 152146 Hom.: 4582 Cov.: 32 AF XY: 0.237 AC XY: 17654 AN XY: 74364

African (AFR) AF: 0.192 AC: 7967 AN: 41504

American (AMR) AF: 0.180 AC: 2753 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3080 AN: 5178

South Asian (SAS) AF: 0.255 AC: 1230 AN: 4816

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15838 AN: 67988

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.208 Hom.: 2025

Bravo AF: 0.225

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.21
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10483084; hg19: chr21-43395324;