dbSNP rs180067: LINC01497:n.66G>A (chr17-69961633-G-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1

The ENST00000455460.6(LINC01497):n.66G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 151,920 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.014 ( 0 hom., cov: 42)

Exomes 𝑓: 0.016 ( 0 hom. )

Consequence

LINC01497
ENST00000455460.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.287

Variant links:

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

LINC01497 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0142 (2154/151738) while in subpopulation NFE AF= 0.0225 (1525/67638). AF 95% confidence interval is 0.0216. There are 0 homozygotes in gnomad4. There are 1061 alleles in male gnomad4 subpopulation. Median coverage is 42. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01497	NR_110874.1 link	n.-74G>A		upstream_gene_variant
LINC01497	NR_110875.1 link	n.-74G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01497	ENST00000455460.6 link	n.66G>A	non_coding_transcript_exon_variant	Exon 1 of 5	3
LINC01497	ENST00000692412.1 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 4
LINC01497	ENST00000702106.1 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0142

AC:

2154

AN:

151620

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00440

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.0288

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0225

Gnomad OTH

AF:

0.0110

GnomAD4 exome

AF:

0.0165

AC:

AN:

182

Hom.:

AF XY:

0.0141

AC XY:

AN XY:

142

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.0145

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0142

AC:

2154

AN:

151738

Hom.:

Cov.:

AF XY:

0.0143

AC XY:

1061

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.00438

Gnomad4 AMR

AF:

0.00478

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.0288

Gnomad4 NFE

AF:

0.0225

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0130

Hom.:

1414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

DANN

Benign

0.91

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over