17-69947399-T-C

Variant names:

• chr17-69947399-T-C
• rs180094
• ENST00000734471.1:n.268+33747T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000734471.1(LINC01497):​n.268+33747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 151,874 control chromosomes in the GnomAD database, including 44,232 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 0.75 (44232 hom., cov: 31)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 4 publications found

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734471.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000734471.1		n.268+33747T>C		intron	N/A
	LINC01497	ENST00000734472.1		n.224+33747T>C		intron	N/A
	LINC01497	ENST00000734473.1		n.227+33747T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114460 AN: 151756 Hom.: 44172 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.754 AC: 114579 AN: 151874 Hom.: 44232 Cov.: 31 AF XY: 0.758 AC XY: 56248 AN XY: 74224

African (AFR) AF: 0.914 AC: 37857 AN: 41422

American (AMR) AF: 0.748 AC: 11406 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2401 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4955 AN: 5162

South Asian (SAS) AF: 0.795 AC: 3823 AN: 4810

European-Finnish (FIN) AF: 0.685 AC: 7211 AN: 10534

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.654 AC: 44438 AN: 67914

Other (OTH) AF: 0.739 AC: 1557 AN: 2106

Alfa AF: 0.601 Hom.: 1804

Bravo AF: 0.770

Asia WGS AF: 0.882 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs180094; hg19: chr17-67943540;