17-11040069-C-T

Position:

• chr17-11040069-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 0.775 in 151,664 control chromosomes in the GnomAD database, including 47,435 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 (47435 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11040069C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117479 AN: 151546 Hom.: 47424 Cov.: 28

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.775 AC: 117513 AN: 151664 Hom.: 47435 Cov.: 28 AF XY: 0.777 AC XY: 57569 AN XY: 74122

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.786

Alfa AF: 0.848 Hom.: 25139

Bravo AF: 0.764

Asia WGS AF: 0.875 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468482; hg19: chr17-10943386;