rs11252887

Variant names:

• chr10-5023056-C-T
• rs11252887

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 0.298 in 152,188 control chromosomes in the GnomAD database, including 6,873 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 0.30 (6873 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.299 AC: 45401 AN: 152070 Hom.: 6872 Cov.: 34

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.298 AC: 45428 AN: 152188 Hom.: 6873 Cov.: 34 AF XY: 0.299 AC XY: 22249 AN XY: 74408

African (AFR) AF: 0.306 AC: 12709 AN: 41516

American (AMR) AF: 0.250 AC: 3820 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2390 AN: 5188

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3170 AN: 10584

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19788 AN: 68006

Other (OTH) AF: 0.290 AC: 613 AN: 2114

Alfa AF: 0.291 Hom.: 26180

Bravo AF: 0.294

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.18
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs11252887; hg19: chr10-5065248;