rs11188147

chr10-95034063-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.416

Alfa AF: 0.355 Hom.: 9494

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11188147; hg19: chr10-96793820;