17-69951455-T-C

Variant names:

• chr17-69951455-T-C
• rs180088
• ENST00000734471.1:n.269-29789T>C

Variant summary

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

The ENST00000734471.1(LINC01497):​n.269-29789T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,842 control chromosomes in the GnomAD database, including 39,492 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 0.72 (39492 hom., cov: 30)
• Consequence: LINC01497 ENST00000734471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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.269-29789T>C		intron_variant	Intron 1 of 3
LINC01497	ENST00000734472.1	n.225-29816T>C		intron_variant	Intron 1 of 3
LINC01497	ENST00000734473.1	n.228-29816T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108838 AN: 151726 Hom.: 39435 Cov.: 30

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.718 AC: 108955 AN: 151842 Hom.: 39492 Cov.: 30 AF XY: 0.722 AC XY: 53518 AN XY: 74170

African (AFR) AF: 0.786 AC: 32565 AN: 41414

American (AMR) AF: 0.732 AC: 11167 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2390 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4956 AN: 5160

South Asian (SAS) AF: 0.795 AC: 3811 AN: 4796

European-Finnish (FIN) AF: 0.688 AC: 7238 AN: 10528

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44401 AN: 67910

Other (OTH) AF: 0.711 AC: 1497 AN: 2106

Alfa AF: 0.689 Hom.: 5466

Bravo AF: 0.727

Asia WGS AF: 0.875 AC: 3044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs180088; hg19: chr17-67947596;