11-69191192-T-G

Position:

• chr11-69191192-T-G

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 0.543 in 152,124 control chromosomes in the GnomAD database, including 23,041 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 0.54 (23041 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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: 0.543 AC: 82478 AN: 152008 Hom.: 23004 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.543 AC: 82572 AN: 152124 Hom.: 23041 Cov.: 33 AF XY: 0.538 AC XY: 40006 AN XY: 74386

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.548

Alfa AF: 0.534 Hom.: 4339

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4495899; hg19: chr11-68958660;