rs10821905

Variant names:

• chr10-50886333-G-A
• rs10821905

Your query was ambiguous. Multiple possible variants found:

• chr10-50886333-G-A
• chr10-50886333-G-T

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 0.201 in 152,048 control chromosomes in the GnomAD database, including 3,324 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 0.20 (3324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.201 AC: 30553 AN: 151930 Hom.: 3317 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.201 AC: 30578 AN: 152048 Hom.: 3324 Cov.: 32 AF XY: 0.203 AC XY: 15110 AN XY: 74334

African (AFR) AF: 0.265 AC: 10987 AN: 41450

American (AMR) AF: 0.133 AC: 2038 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3472

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5188

South Asian (SAS) AF: 0.213 AC: 1030 AN: 4826

European-Finnish (FIN) AF: 0.285 AC: 3007 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11973 AN: 67964

Other (OTH) AF: 0.191 AC: 404 AN: 2112

Alfa AF: 0.178 Hom.: 3587

Bravo AF: 0.191

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.013
DANN	Benign	0.16
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10821905; hg19: chr10-52646093;