chr10-52762874-C-T

Variant names:

• chr10-52762874-C-T
• rs11003120

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 0.127 in 152,130 control chromosomes in the GnomAD database, including 1,513 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 0.13 (1513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.127 AC: 19348 AN: 152012 Hom.: 1513 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.127 AC: 19337 AN: 152130 Hom.: 1513 Cov.: 32 AF XY: 0.128 AC XY: 9498 AN XY: 74342

African (AFR) AF: 0.0359 AC: 1489 AN: 41516

American (AMR) AF: 0.102 AC: 1555 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3466

East Asian (EAS) AF: 0.146 AC: 757 AN: 5170

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1825 AN: 10560

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11635 AN: 68002

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.164 Hom.: 1156

Bravo AF: 0.113

Asia WGS AF: 0.167 AC: 579 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11003120; hg19: chr10-54522634;