Variant 5-54684172-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_104658.1(LINC02998):n.401-17997C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,098 control chromosomes in the GnomAD database, including 47,032 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 0.77 ( 47032 hom., cov: 33)

Consequence

LINC02998
NR_104658.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.156

Variant links:

Genes affected

ENSG00000287367 (HGNC:):

ENSG00000287367 links:

LINC02998 (HGNC:56114): (long intergenic non-protein coding RNA 2998)

LINC02998 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02998	NR_104658.1 link	n.401-17997C>T		intron_variant
LINC02998	NR_104659.1 link	n.159-17997C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287367	ENST00000662448.1 link	n.1714-7788G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

117486

AN:

151980

Hom.:

47012

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.808

Gnomad AMR

AF:

0.781

Gnomad ASJ

AF:

0.800

Gnomad EAS

AF:

0.846

Gnomad SAS

AF:

0.851

Gnomad FIN

AF:

0.946

Gnomad MID

AF:

0.807

Gnomad NFE

AF:

0.870

Gnomad OTH

AF:

0.779

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

GnomAD4 genome

AF:

0.773

AC:

117547

AN:

152098

Hom.:

47032

Cov.:

AF XY:

0.777

AC XY:

57828

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.545

Gnomad4 AMR

AF:

0.780

Gnomad4 ASJ

AF:

0.800

Gnomad4 EAS

AF:

0.846

Gnomad4 SAS

AF:

0.851

Gnomad4 FIN

AF:

0.946

Gnomad4 NFE

AF:

0.870

Gnomad4 OTH

AF:

0.781

Alfa

AF:

0.851

Hom.:

73617

Bravo

AF:

0.749

Asia WGS

AF:

0.845

AC:

2939

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.5

DANN

Benign

0.76

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