17-69947273-T-G

Variant names:

• chr17-69947273-T-G
• rs180095
• ENST00000734471.1:n.268+33621T>G

Variant summary

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

The ENST00000734471.1(LINC01497):​n.268+33621T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 150,206 control chromosomes in the GnomAD database, including 43,741 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 0.75 (43741 hom., cov: 24)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 7 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=-0.99).
• 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000734471.1		n.268+33621T>G		intron	N/A
	LINC01497	ENST00000734472.1		n.224+33621T>G		intron	N/A
	LINC01497	ENST00000734473.1		n.227+33621T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 113211 AN: 150090 Hom.: 43682 Cov.: 24

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.754 AC: 113328 AN: 150206 Hom.: 43741 Cov.: 24 AF XY: 0.758 AC XY: 55516 AN XY: 73224

African (AFR) AF: 0.914 AC: 37319 AN: 40830

American (AMR) AF: 0.748 AC: 11272 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2393 AN: 3454

East Asian (EAS) AF: 0.959 AC: 4826 AN: 5030

South Asian (SAS) AF: 0.794 AC: 3719 AN: 4682

European-Finnish (FIN) AF: 0.685 AC: 7034 AN: 10264

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.655 AC: 44299 AN: 67606

Other (OTH) AF: 0.740 AC: 1536 AN: 2076

Alfa AF: 0.712 Hom.: 5094

Bravo AF: 0.770

Asia WGS AF: 0.882 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.68
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs180095; hg19: chr17-67943414;