Variant 5-126776477-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_134485.1(LMNB1-DT):n.10A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 152,260 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 104 hom., cov: 33)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

LMNB1-DT
NR_134485.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.11

Variant links:

Genes affected

LMNB1-DT (HGNC:53089): (LMNB1 divergent transcript)

LMNB1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-126776477-T-C is Benign according to our data. Variant chr5-126776477-T-C is described in ClinVar as [Benign]. Clinvar id is 1235155.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMNB1-DT	NR_134485.1 linkuse as main transcript	n.10A>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMNB1-DT	ENST00000509185.2 linkuse as main transcript	n.10A>G		non_coding_transcript_exon_variant	1/4	5

Frequencies

GnomAD3 genomes

AF:

0.0314

AC:

4770

AN:

152138

Hom.:

104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0538

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.0311

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00455

Gnomad FIN

AF:

0.0332

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0205

Gnomad OTH

AF:

0.0406

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.0313

AC:

4766

AN:

152256

Hom.:

104

Cov.:

AF XY:

0.0307

AC XY:

2282

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0537

Gnomad4 AMR

AF:

0.0352

Gnomad4 ASJ

AF:

0.0311

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00435

Gnomad4 FIN

AF:

0.0332

Gnomad4 NFE

AF:

0.0205

Gnomad4 OTH

AF:

0.0407

Alfa

AF:

0.0322

Hom.:

Bravo

AF:

0.0325

Asia WGS

AF:

0.00779

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.79

DANN

Benign

0.48

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over