17-69362956-C-T

Position:

• chr17-69362956-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 17-69362956-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,200 control chromosomes in the GnomAD database, including 1,126 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 0.11 (1126 hom., cov: 32)
• Consequence: LOC105371879 XR_934950.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

LOC105371879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371879	XR_934950.3			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16009 AN: 152082 Hom.: 1125 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.105 AC: 16012 AN: 152200 Hom.: 1126 Cov.: 32 AF XY: 0.102 AC XY: 7625 AN XY: 74406

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0511

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.103

Alfa AF: 0.126 Hom.: 941

Bravo AF: 0.101

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560271; hg19: chr17-67359097;