11-69208652-T-C

Position:

• chr11-69208652-T-C

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 0.65 in 152,054 control chromosomes in the GnomAD database, including 32,648 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 0.65 (32648 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69208652T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98723 AN: 151936 Hom.: 32611 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.650 AC: 98816 AN: 152054 Hom.: 32648 Cov.: 32 AF XY: 0.649 AC XY: 48276 AN XY: 74332

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.661

Alfa AF: 0.611 Hom.: 4783

Bravo AF: 0.649

Asia WGS AF: 0.589 AC: 2047 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	0.095
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4495900; hg19: chr11-68976119;