rs180113

Variant names:

• chr17-69928988-T-C
• rs180113
• ENST00000734471.1:n.268+15336T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000734471.1(LINC01497):​n.268+15336T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,960 control chromosomes in the GnomAD database, including 35,377 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 0.68 (35377 hom., cov: 31)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01497	ENST00000734471.1	n.268+15336T>C		intron_variant	Intron 1 of 3
LINC01497	ENST00000734472.1	n.224+15336T>C		intron_variant	Intron 1 of 3
LINC01497	ENST00000734473.1	n.227+15336T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103330 AN: 151842 Hom.: 35343 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.681 AC: 103413 AN: 151960 Hom.: 35377 Cov.: 31 AF XY: 0.686 AC XY: 50980 AN XY: 74276

African (AFR) AF: 0.662 AC: 27422 AN: 41398

American (AMR) AF: 0.716 AC: 10934 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4966 AN: 5176

South Asian (SAS) AF: 0.790 AC: 3797 AN: 4808

European-Finnish (FIN) AF: 0.685 AC: 7240 AN: 10566

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44302 AN: 67956

Other (OTH) AF: 0.682 AC: 1437 AN: 2106

Alfa AF: 0.657 Hom.: 4085

Bravo AF: 0.685

Asia WGS AF: 0.863 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs180113; hg19: chr17-67925129;