17-69954325-A-G

Variant names:

• chr17-69954325-A-G
• rs180084
• ENST00000734471.1:n.269-26919A>G

Variant summary

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

The ENST00000734471.1(LINC01497):​n.269-26919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,048 control chromosomes in the GnomAD database, including 39,337 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 (39337 hom., cov: 32)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000734471.1		n.269-26919A>G		intron	N/A
	LINC01497	ENST00000734472.1		n.225-26946A>G		intron	N/A
	LINC01497	ENST00000734473.1		n.228-26946A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108715 AN: 151930 Hom.: 39280 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.959

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: 0.716 AC: 108832 AN: 152048 Hom.: 39337 Cov.: 32 AF XY: 0.720 AC XY: 53513 AN XY: 74328

African (AFR) AF: 0.786 AC: 32589 AN: 41484

American (AMR) AF: 0.725 AC: 11070 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4978 AN: 5188

South Asian (SAS) AF: 0.792 AC: 3825 AN: 4828

European-Finnish (FIN) AF: 0.690 AC: 7273 AN: 10548

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

European-Non Finnish (NFE) AF: 0.653 AC: 44331 AN: 67940

Other (OTH) AF: 0.702 AC: 1484 AN: 2114

Alfa AF: 0.557 Hom.: 1457

Bravo AF: 0.724

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	-0.90
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs180084; hg19: chr17-67950466;