11-69634308-G-C

Position:

• chr11-69634308-G-C

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 0.368 in 151,968 control chromosomes in the GnomAD database, including 10,672 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 0.37 (10672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55842 AN: 151850 Hom.: 10660 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.368 AC: 55871 AN: 151968 Hom.: 10672 Cov.: 32 AF XY: 0.364 AC XY: 27069 AN XY: 74282

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.353

Alfa AF: 0.246 Hom.: 672

Bravo AF: 0.378

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667515; hg19: chr11-69449076;