rs10999169

Variant names:

• chr10-70171256-C-T
• rs10999169

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 0.38 in 151,976 control chromosomes in the GnomAD database, including 12,027 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 0.38 (12027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.381 AC: 57803 AN: 151856 Hom.: 12021 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.380 AC: 57818 AN: 151976 Hom.: 12027 Cov.: 32 AF XY: 0.382 AC XY: 28360 AN XY: 74266

African (AFR) AF: 0.204 AC: 8458 AN: 41452

American (AMR) AF: 0.501 AC: 7649 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2895 AN: 5170

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4818

European-Finnish (FIN) AF: 0.394 AC: 4151 AN: 10536

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29705 AN: 67934

Other (OTH) AF: 0.400 AC: 844 AN: 2110

Alfa AF: 0.423 Hom.: 55786

Bravo AF: 0.386

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10999169; hg19: chr10-71931012;