11-69513996-C-T

Position:

• chr11-69513996-C-T

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 0.135 in 152,136 control chromosomes in the GnomAD database, including 1,512 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 0.13 (1512 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 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: 0.135 AC: 20500 AN: 152018 Hom.: 1512 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00830

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.135 AC: 20512 AN: 152136 Hom.: 1512 Cov.: 31 AF XY: 0.136 AC XY: 10132 AN XY: 74370

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00793

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.134

Alfa AF: 0.140 Hom.: 3688

Bravo AF: 0.124

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs614367; hg19: chr11-69328764;