rs180092

Variant names:

• chr17-69948273-G-A
• rs180092
• ENST00000734471.1:n.269-32971G>A

Variant summary

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

The ENST00000734471.1(LINC01497):​n.269-32971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 149,388 control chromosomes in the GnomAD database, including 5,164 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 0.25 (5164 hom., cov: 27)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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.269-32971G>A		intron	N/A
	LINC01497	ENST00000734472.1		n.225-32998G>A		intron	N/A
	LINC01497	ENST00000734473.1		n.228-32998G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 37432 AN: 149328 Hom.: 5169 Cov.: 27

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.251 AC: 37437 AN: 149388 Hom.: 5164 Cov.: 27 AF XY: 0.255 AC XY: 18529 AN XY: 72664

African (AFR) AF: 0.156 AC: 6335 AN: 40660

American (AMR) AF: 0.315 AC: 4709 AN: 14944

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 936 AN: 3450

East Asian (EAS) AF: 0.533 AC: 2680 AN: 5024

South Asian (SAS) AF: 0.269 AC: 1265 AN: 4700

European-Finnish (FIN) AF: 0.321 AC: 3146 AN: 9792

Middle Eastern (MID) AF: 0.327 AC: 91 AN: 278

European-Non Finnish (NFE) AF: 0.258 AC: 17402 AN: 67574

Other (OTH) AF: 0.287 AC: 592 AN: 2064

Alfa AF: 0.250 Hom.: 1704

Bravo AF: 0.252

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.76
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs180092; hg19: chr17-67944414;