17-14947369-G-T

Position:

• chr17-14947369-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 0.469 in 152,062 control chromosomes in the GnomAD database, including 18,732 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 (18732 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14947369G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02096	ENST00000664152.1	n.910-448G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71166 AN: 151944 Hom.: 18692 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.469 AC: 71250 AN: 152062 Hom.: 18732 Cov.: 33 AF XY: 0.465 AC XY: 34518 AN XY: 74312

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.445

Alfa AF: 0.373 Hom.: 5130

Bravo AF: 0.472

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521290; hg19: chr17-14850686;