rs11188172

Variant names:

• chr10-95071450-C-T
• rs11188172

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 0.182 in 152,112 control chromosomes in the GnomAD database, including 3,227 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 0.18 (3227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 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: 0.182 AC: 27669 AN: 151994 Hom.: 3222 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.182 AC: 27672 AN: 152112 Hom.: 3227 Cov.: 32 AF XY: 0.185 AC XY: 13757 AN XY: 74380

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.163

Alfa AF: 0.214 Hom.: 792

Bravo AF: 0.170

Asia WGS AF: 0.118 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.054
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11188172; hg19: chr10-96831207;