Variant 18-51425959-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000578152.5(LINC01630):n.216+33702T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,060 control chromosomes in the GnomAD database, including 20,442 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 0.49 ( 20442 hom., cov: 33)

Consequence

LINC01630
ENST00000578152.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Variant links:

Genes affected

LINC01630 (HGNC:52295): (long intergenic non-protein coding RNA 1630)

LINC01630 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01630	NR_040074.1 link	n.216+33702T>C		intron_variant
LINC01630	NR_040075.1 link	n.216+33702T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01630	ENST00000435144.7 link	n.219+33702T>C	intron_variant	5
LINC01630	ENST00000578152.5 link	n.216+33702T>C	intron_variant	2
LINC01630	ENST00000580841.1 link	n.216+33702T>C	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74711

AN:

151940

Hom.:

20428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.568

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.554

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.484

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

GnomAD4 genome

AF:

0.492

AC:

74748

AN:

152060

Hom.:

20442

Cov.:

AF XY:

0.499

AC XY:

37100

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.568

Gnomad4 EAS

AF:

0.752

Gnomad4 SAS

AF:

0.675

Gnomad4 FIN

AF:

0.554

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.517

Hom.:

2674

Bravo

AF:

0.484

Asia WGS

AF:

0.643

AC:

2232

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.6

DANN

Benign

0.65

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