chr10-52777687-C-T

Variant names:

• chr10-52777687-C-T
• rs11003132

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 0.198 in 152,098 control chromosomes in the GnomAD database, including 3,259 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 (3259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 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: 0.199 AC: 30188 AN: 151980 Hom.: 3264 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.198 AC: 30188 AN: 152098 Hom.: 3259 Cov.: 32 AF XY: 0.198 AC XY: 14730 AN XY: 74320

African (AFR) AF: 0.115 AC: 4764 AN: 41506

American (AMR) AF: 0.154 AC: 2358 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3468

East Asian (EAS) AF: 0.167 AC: 865 AN: 5166

South Asian (SAS) AF: 0.239 AC: 1148 AN: 4810

European-Finnish (FIN) AF: 0.265 AC: 2796 AN: 10554

Middle Eastern (MID) AF: 0.207 AC: 60 AN: 290

European-Non Finnish (NFE) AF: 0.252 AC: 17122 AN: 67992

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.198 Hom.: 2764

Bravo AF: 0.181

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.51
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11003132; hg19: chr10-54537447;