rs11188147

Variant names:

• chr10-95034063-C-T
• rs11188147

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 0.378 in 151,998 control chromosomes in the GnomAD database, including 11,221 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 (11221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.378 AC: 57348 AN: 151880 Hom.: 11205 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.378 AC: 57399 AN: 151998 Hom.: 11221 Cov.: 32 AF XY: 0.377 AC XY: 28043 AN XY: 74294

African (AFR) AF: 0.475 AC: 19658 AN: 41422

American (AMR) AF: 0.322 AC: 4911 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1442 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2036 AN: 5170

South Asian (SAS) AF: 0.399 AC: 1924 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3355 AN: 10562

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22677 AN: 67966

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.360 Hom.: 14575

Bravo AF: 0.382

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.24
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11188147; hg19: chr10-96793820;