17-69924202-A-T

Variant names:

• chr17-69924202-A-T
• rs180126
• ENST00000734471.1:n.268+10550A>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+10550A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,094 control chromosomes in the GnomAD database, including 4,561 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 (4561 hom., cov: 30)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 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+10550A>T		intron	N/A
	LINC01497	ENST00000734472.1		n.224+10550A>T		intron	N/A
	LINC01497	ENST00000734473.1		n.227+10550A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 32890 AN: 150978 Hom.: 4567 Cov.: 30

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.218 AC: 32885 AN: 151094 Hom.: 4561 Cov.: 30 AF XY: 0.224 AC XY: 16510 AN XY: 73778

African (AFR) AF: 0.0553 AC: 2288 AN: 41406

American (AMR) AF: 0.305 AC: 4612 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 940 AN: 3448

East Asian (EAS) AF: 0.526 AC: 2633 AN: 5010

South Asian (SAS) AF: 0.263 AC: 1251 AN: 4758

European-Finnish (FIN) AF: 0.307 AC: 3206 AN: 10452

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17024 AN: 67578

Other (OTH) AF: 0.267 AC: 560 AN: 2098

Alfa AF: 0.224 Hom.: 464

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.39
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs180126; hg19: chr17-67920343; COSMIC: COSV64780794;