rs180097

Variant names:

• chr17-69944362-G-A
• rs180097
• ENST00000734471.1:n.268+30710G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-69944362-G-A
• chr17-69944362-G-T

Variant summary

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

The ENST00000734471.1(LINC01497):​n.268+30710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,046 control chromosomes in the GnomAD database, including 4,764 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 0.22 (4764 hom., cov: 32)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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.268+30710G>A		intron	N/A
	LINC01497	ENST00000734472.1		n.224+30710G>A		intron	N/A
	LINC01497	ENST00000734473.1		n.227+30710G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33716 AN: 151930 Hom.: 4770 Cov.: 32

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.222 AC: 33711 AN: 152046 Hom.: 4764 Cov.: 32 AF XY: 0.228 AC XY: 16943 AN XY: 74326

African (AFR) AF: 0.0575 AC: 2387 AN: 41518

American (AMR) AF: 0.306 AC: 4670 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2737 AN: 5156

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3323 AN: 10562

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17444 AN: 67952

Other (OTH) AF: 0.265 AC: 559 AN: 2106

Alfa AF: 0.116 Hom.: 214

Bravo AF: 0.220

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.054
DANN	Benign	0.46
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs180097; hg19: chr17-67940503;