Variant 3-165337681-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000470138.5(LINC01322):n.201-45114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,784 control chromosomes in the GnomAD database, including 34,117 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 0.66 ( 34117 hom., cov: 33)

Consequence

LINC01322
ENST00000470138.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.843

Variant links:

Genes affected

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

LINC01322 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LINC01322	NR_125764.2 link	n.213-36578C>T	intron_variant
LINC01322	NR_174098.1 link	n.213-7791C>T	intron_variant
LINC01322	NR_174099.1 link	n.213-7791C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01322	ENST00000470138.5 link	n.201-45114C>T	intron_variant	4
LINC01322	ENST00000494915.2 link	n.165-7791C>T	intron_variant	4
LINC01322	ENST00000498616.6 link	n.203-7791C>T	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100442

AN:

151666

Hom.:

34095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.697

Gnomad EAS

AF:

0.859

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.671

Gnomad MID

AF:

0.723

Gnomad NFE

AF:

0.703

Gnomad OTH

AF:

0.659

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

GnomAD4 genome

AF:

0.662

AC:

100497

AN:

151784

Hom.:

34117

Cov.:

AF XY:

0.664

AC XY:

49228

AN XY:

74144

show subpopulations

Gnomad4 AFR

AF:

0.563

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.697

Gnomad4 EAS

AF:

0.859

Gnomad4 SAS

AF:

0.797

Gnomad4 FIN

AF:

0.671

Gnomad4 NFE

AF:

0.703

Gnomad4 OTH

AF:

0.661

Alfa

AF:

0.659

Hom.:

6158

Bravo

AF:

0.646

Asia WGS

AF:

0.784

AC:

2728

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.62

DANN

Benign

0.64

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