rs180133

Variant names:

• chr17-69922075-A-G
• rs180133
• ENST00000734471.1:n.268+8423A>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+8423A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,046 control chromosomes in the GnomAD database, including 34,995 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 (34995 hom., cov: 32)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 10 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=-0.85).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000734471.1		n.268+8423A>G		intron	N/A
	LINC01497	ENST00000734472.1		n.224+8423A>G		intron	N/A
	LINC01497	ENST00000734473.1		n.227+8423A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102781 AN: 151928 Hom.: 34961 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.677 AC: 102864 AN: 152046 Hom.: 34995 Cov.: 32 AF XY: 0.683 AC XY: 50723 AN XY: 74314

African (AFR) AF: 0.649 AC: 26924 AN: 41478

American (AMR) AF: 0.715 AC: 10912 AN: 15270

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

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

South Asian (SAS) AF: 0.789 AC: 3803 AN: 4820

European-Finnish (FIN) AF: 0.684 AC: 7223 AN: 10556

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

European-Non Finnish (NFE) AF: 0.652 AC: 44288 AN: 67958

Other (OTH) AF: 0.678 AC: 1434 AN: 2114

Alfa AF: 0.656 Hom.: 4243

Bravo AF: 0.680

Asia WGS AF: 0.860 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.67
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs180133; hg19: chr17-67918216;