Variant chr5-142747191-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000432677.2(LINC01844):n.158+1469C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,128 control chromosomes in the GnomAD database, including 15,837 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 0.33 ( 15837 hom., cov: 32)

Consequence

LINC01844
ENST00000432677.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Variant links:

Genes affected

LINC01844 (HGNC:):

LINC01844 links:

LINC01844 (HGNC:52660): (long intergenic non-protein coding RNA 1844)

LINC01844 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01844	NR_110558.1 link	n.119+1473C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01844	ENST00000432677.2 link	n.158+1469C>G	intron_variant	1
LINC01844	ENST00000652722.1 link	n.136+1469C>G	intron_variant
LINC01844	ENST00000652991.1 link	n.170+1469C>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

50028

AN:

152010

Hom.:

15779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.297

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

GnomAD4 genome

AF:

0.330

AC:

50137

AN:

152128

Hom.:

15837

Cov.:

AF XY:

0.330

AC XY:

24505

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.823

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.372

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0880

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.216

Hom.:

1154

Bravo

AF:

0.366

Asia WGS

AF:

0.374

AC:

1302

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.0

DANN

Benign

0.72

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