11-69517902-A-G

Variant names:

• chr11-69517902-A-G
• rs657686

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 0.119 in 152,244 control chromosomes in the GnomAD database, including 1,184 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 0.12 (1184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 15 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 (SAS) allele frequency at 95% confidence interval = 0.152 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: 0.119 AC: 18145 AN: 152126 Hom.: 1183 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.119 AC: 18163 AN: 152244 Hom.: 1184 Cov.: 32 AF XY: 0.121 AC XY: 9023 AN XY: 74448

African (AFR) AF: 0.126 AC: 5215 AN: 41544

American (AMR) AF: 0.0832 AC: 1273 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3468

East Asian (EAS) AF: 0.00715 AC: 37 AN: 5178

South Asian (SAS) AF: 0.162 AC: 781 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1550 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8499 AN: 68004

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.124 Hom.: 624

Bravo AF: 0.110

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs657686; hg19: chr11-69332670;