ENST00000734471.1:n.269-22273T>C

Variant names:

• chr17-69958971-T-C
• rs180075
• ENST00000734471.1:n.269-22273T>C

Variant summary

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

The ENST00000734471.1(LINC01497):​n.269-22273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,116 control chromosomes in the GnomAD database, including 41,154 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 0.73 (41154 hom., cov: 32)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 6 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=-0.92).
• 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

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.269-22273T>C		intron	N/A
	LINC01497	ENST00000734472.1		n.225-22300T>C		intron	N/A
	LINC01497	ENST00000734473.1		n.228-22300T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111317 AN: 151998 Hom.: 41104 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.733 AC: 111427 AN: 152116 Hom.: 41154 Cov.: 32 AF XY: 0.736 AC XY: 54742 AN XY: 74358

African (AFR) AF: 0.790 AC: 32814 AN: 41512

American (AMR) AF: 0.734 AC: 11219 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4970 AN: 5176

South Asian (SAS) AF: 0.850 AC: 4088 AN: 4808

European-Finnish (FIN) AF: 0.698 AC: 7374 AN: 10570

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46069 AN: 67982

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.702 Hom.: 4873

Bravo AF: 0.739

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.31
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs180075; hg19: chr17-67955112;