Genetic Variant LINC01697:n.714G>T (chr21-28103172-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000458316.1(LINC01697):n.714G>T 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 0.0869 in 152,092 control chromosomes in the GnomAD database, including 660 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 0.087 ( 660 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LINC01697
ENST00000458316.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.947

Variant links:

Genes affected

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

LINC01697 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126011.1 link	n.796G>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01697	NR_126010.1 link	n.344+403G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01697	ENST00000458316.1 link	n.714G>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC01697	ENST00000436878.1 link	n.754G>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC01697	ENST00000657256.1 link	n.832G>T	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0869

AC:

13211

AN:

151974

Hom.:

657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0551

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.0133

Gnomad SAS

AF:

0.0351

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0834

Gnomad OTH

AF:

0.0715

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.0869

AC:

13221

AN:

152092

Hom.:

660

Cov.:

AF XY:

0.0855

AC XY:

6353

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0550

Gnomad4 ASJ

AF:

0.0412

Gnomad4 EAS

AF:

0.0133

Gnomad4 SAS

AF:

0.0351

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.0833

Gnomad4 OTH

AF:

0.0708

Alfa

AF:

0.0902

Hom.:

Bravo

AF:

0.0846

Asia WGS

AF:

0.0290

AC:

101

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

0.53

DANN

Benign

0.65

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