rs11153162

chr6-96756418-C-Achr6-96756418-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 0.172 in 151,618 control chromosomes in the GnomAD database, including 2,471 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 0.17 (2471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 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: 0.172 AC: 26031 AN: 151500 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.172 AC: 26038 AN: 151618 Hom.: 2471 Cov.: 32 AF XY: 0.170 AC XY: 12617 AN XY: 74114

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.181

Alfa AF: 0.173 Hom.: 1317

Bravo AF: 0.166

Asia WGS AF: 0.0690 AC: 239 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.2
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11153162; hg19: chr6-97204294;