Variant 7-20957333-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_126381.1(LINC01162):n.152-63533delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 49314 hom., cov: 0)

Consequence

LINC01162
NR_126381.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Variant links:

Genes affected

LINC01162 (HGNC:):

LINC01162 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01162	NR_126381.1 linkuse as main transcript	n.152-63533delG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2 linkuse as main transcript	n.152-63533delG		intron_variant		5
LINC01162	ENST00000661032.1 linkuse as main transcript	n.207-3345delG		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.804

AC:

122162

AN:

151962

Hom.:

49265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.854

Gnomad AMI

AF:

0.841

Gnomad AMR

AF:

0.850

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.762

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.764

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.831

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

GnomAD4 genome

AF:

0.804

AC:

122270

AN:

152080

Hom.:

49314

Cov.:

AF XY:

0.803

AC XY:

59707

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.854

Gnomad4 AMR

AF:

0.850

Gnomad4 ASJ

AF:

0.785

Gnomad4 EAS

AF:

0.762

Gnomad4 SAS

AF:

0.795

Gnomad4 FIN

AF:

0.764

Gnomad4 NFE

AF:

0.772

Gnomad4 OTH

AF:

0.831

Alfa

AF:

0.785

Hom.:

5717

Bravo

AF:

0.815

Asia WGS

AF:

0.796

AC:

2765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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