11-69705233-T-A

Variant names:

• chr11-69705233-T-A
• rs1789364

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 0.551 in 151,842 control chromosomes in the GnomAD database, including 24,366 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 0.55 (24366 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.551 AC: 83550 AN: 151724 Hom.: 24351 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.551 AC: 83598 AN: 151842 Hom.: 24366 Cov.: 31 AF XY: 0.551 AC XY: 40914 AN XY: 74190

African (AFR) AF: 0.347 AC: 14371 AN: 41406

American (AMR) AF: 0.716 AC: 10946 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3953 AN: 5116

South Asian (SAS) AF: 0.550 AC: 2648 AN: 4812

European-Finnish (FIN) AF: 0.533 AC: 5635 AN: 10564

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.612 AC: 41546 AN: 67880

Other (OTH) AF: 0.616 AC: 1294 AN: 2102

Alfa AF: 0.564 Hom.: 3145

Bravo AF: 0.560

Asia WGS AF: 0.648 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.75
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs1789364; hg19: chr11-69520001;