11-69048055-C-T

Position:

• chr11-69048055-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 0.77 in 152,088 control chromosomes in the GnomAD database, including 50,561 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 0.77 (50561 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69048055C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117087 AN: 151970 Hom.: 50570 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.770 AC: 117101 AN: 152088 Hom.: 50561 Cov.: 32 AF XY: 0.768 AC XY: 57103 AN XY: 74346

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.809

Alfa AF: 0.936 Hom.: 115465

Bravo AF: 0.727

Asia WGS AF: 0.697 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10750836; hg19: chr11-68815523;