Variant chr1-47416226-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NR_126355.1(LINC01389):n.29-6325C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 942,146 control chromosomes in the GnomAD database, including 1,008 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 111 hom., cov: 31)

Exomes 𝑓: 0.044 ( 897 hom. )

Consequence

LINC01389
NR_126355.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.04

Variant links:

Genes affected

LINC01389 (HGNC:):

LINC01389 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-47416226-G-T is Benign according to our data. Variant chr1-47416226-G-T is described in ClinVar as [Benign]. Clinvar id is 1296404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01389	NR_126355.1 linkuse as main transcript	n.29-6325C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0332

AC:

5016

AN:

151200

Hom.:

111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.0349

Gnomad ASJ

AF:

0.0211

Gnomad EAS

AF:

0.000395

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.0320

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0516

Gnomad OTH

AF:

0.0429

GnomAD4 exome

AF:

0.0444

AC:

35112

AN:

790838

Hom.:

897

Cov.:

AF XY:

0.0440

AC XY:

16706

AN XY:

379934

show subpopulations

Gnomad4 AFR exome

AF:

0.00601

Gnomad4 AMR exome

AF:

0.0310

Gnomad4 ASJ exome

AF:

0.0190

Gnomad4 EAS exome

AF:

0.0000510

Gnomad4 SAS exome

AF:

0.00296

Gnomad4 FIN exome

AF:

0.0356

Gnomad4 NFE exome

AF:

0.0489

Gnomad4 OTH exome

AF:

0.0357

GnomAD4 genome

AF:

0.0331

AC:

5015

AN:

151308

Hom.:

111

Cov.:

AF XY:

0.0309

AC XY:

2288

AN XY:

73958

show subpopulations

Gnomad4 AFR

AF:

0.0105

Gnomad4 AMR

AF:

0.0349

Gnomad4 ASJ

AF:

0.0211

Gnomad4 EAS

AF:

0.000396

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.0320

Gnomad4 NFE

AF:

0.0516

Gnomad4 OTH

AF:

0.0424

Alfa

AF:

0.0278

Hom.:

Bravo

AF:

0.0323

Asia WGS

AF:

0.00260

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over