11-69689509-T-A

Variant names:

• chr11-69689509-T-A
• rs1192923

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 0.567 in 151,784 control chromosomes in the GnomAD database, including 25,827 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 0.57 (25827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.567 AC: 86020 AN: 151666 Hom.: 25824 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.567 AC: 86047 AN: 151784 Hom.: 25827 Cov.: 32 AF XY: 0.573 AC XY: 42469 AN XY: 74174

African (AFR) AF: 0.388 AC: 15979 AN: 41224

American (AMR) AF: 0.506 AC: 7704 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3468

East Asian (EAS) AF: 0.887 AC: 4586 AN: 5170

South Asian (SAS) AF: 0.590 AC: 2839 AN: 4814

European-Finnish (FIN) AF: 0.751 AC: 7944 AN: 10584

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43027 AN: 67980

Other (OTH) AF: 0.577 AC: 1212 AN: 2102

Alfa AF: 0.585 Hom.: 2863

Bravo AF: 0.541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.31
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1192923; hg19: chr11-69504277; COSMIC: COSV69616266;