11-68682735-C-T

Position:

• chr11-68682735-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 0.661 in 152,006 control chromosomes in the GnomAD database, including 34,922 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 0.66 (34922 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68682735C>T		intergenic_region
LOC107984343	XR_001748281.1	n.230+5106G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100374 AN: 151888 Hom.: 34910 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.661 AC: 100412 AN: 152006 Hom.: 34922 Cov.: 31 AF XY: 0.672 AC XY: 49910 AN XY: 74298

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.664

Alfa AF: 0.679 Hom.: 4664

Bravo AF: 0.634

Asia WGS AF: 0.802 AC: 2791 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	0.069
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948854; hg19: chr11-68450203;