17-69951682-C-G

Variant names:

• chr17-69951682-C-G
• rs180087
• ENST00000734471.1:n.269-29562C>G

Variant summary

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

The ENST00000734471.1(LINC01497):​n.269-29562C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,006 control chromosomes in the GnomAD database, including 39,287 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 0.72 (39287 hom., cov: 31)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 5 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=-0.82).
• 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.269-29562C>G		intron	N/A
	LINC01497	ENST00000734472.1		n.225-29589C>G		intron	N/A
	LINC01497	ENST00000734473.1		n.228-29589C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108613 AN: 151888 Hom.: 39230 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.715 AC: 108730 AN: 152006 Hom.: 39287 Cov.: 31 AF XY: 0.719 AC XY: 53443 AN XY: 74286

African (AFR) AF: 0.785 AC: 32567 AN: 41486

American (AMR) AF: 0.725 AC: 11074 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4951 AN: 5158

South Asian (SAS) AF: 0.793 AC: 3808 AN: 4802

European-Finnish (FIN) AF: 0.690 AC: 7281 AN: 10558

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44289 AN: 67954

Other (OTH) AF: 0.702 AC: 1478 AN: 2106

Alfa AF: 0.583 Hom.: 1755

Bravo AF: 0.723

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.32
DANN	Benign	0.85
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs180087; hg19: chr17-67947823;