chr11-68141915-G-T

Position:

• chr11-68141915-G-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 0.467 in 152,018 control chromosomes in the GnomAD database, including 19,639 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 0.47 (19639 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68141915G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70976 AN: 151900 Hom.: 19629 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.467 AC: 70987 AN: 152018 Hom.: 19639 Cov.: 32 AF XY: 0.475 AC XY: 35315 AN XY: 74274

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.521

Alfa AF: 0.504 Hom.: 2663

Bravo AF: 0.461

Asia WGS AF: 0.628 AC: 2184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.47
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228145; hg19: chr11-67909382;