11-69191192-T-G

Variant names:

• chr11-69191192-T-G
• rs4495899

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.671 AC: 27861 AN: 41514

American (AMR) AF: 0.478 AC: 7315 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1609 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2981 AN: 5150

South Asian (SAS) AF: 0.320 AC: 1546 AN: 4828

European-Finnish (FIN) AF: 0.512 AC: 5429 AN: 10600

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33922 AN: 67946

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

Alfa AF: 0.529 Hom.: 7780

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4495899; hg19: chr11-68958660;