Variant 16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGT details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000601250.1(LINC01082):n.232+1361_232+1362delGT 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 0.16 ( 1972 hom., cov: 0)

Consequence

LINC01082
ENST00000601250.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.806

Variant links:

Genes affected

ENSG00000268505 (HGNC:):

ENSG00000268505 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01082	NR_103859.1 linkuse as main transcript	n.232+1361_232+1362delGT		intron_variant
LOC124903743	XR_007065164.1 linkuse as main transcript	n.628-567_628-566delAC		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000268505	ENST00000599841.1 linkuse as main transcript	n.25-567_25-566delAC	intron_variant	4
LINC01082	ENST00000601250.1 linkuse as main transcript	n.232+1361_232+1362delGT	intron_variant	2
LINC01082	ENST00000669926.2 linkuse as main transcript	n.459+1361_459+1362delGT	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

23564

AN:

147528

Hom.:

1964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.0920

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.160

AC:

23608

AN:

147634

Hom.:

1972

Cov.:

AF XY:

0.159

AC XY:

11418

AN XY:

71816

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.177

Gnomad4 ASJ

AF:

0.113

Gnomad4 EAS

AF:

0.159

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.0920

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.166

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