11-69634308-G-C

Variant names:

• chr11-69634308-G-C
• rs667515

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;