Variant 5-36137518-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001007527.2(LMBRD2):c.369-77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 902,712 control chromosomes in the GnomAD database, including 419,145 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 0.94 ( 67843 hom., cov: 32)

Exomes 𝑓: 0.96 ( 351302 hom. )

Consequence

LMBRD2
NM_001007527.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Variant links:

Genes affected

LMBRD2 (HGNC:25287): (LMBR1 domain containing 2) Involved in adrenergic receptor signaling pathway. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

LMBRD2 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMBRD2	NM_001007527.2 linkuse as main transcript	c.369-77T>C		intron_variant		ENST00000296603.5	NP_001007528.1	Q68DH5
LMBRD2	XM_011514162.3 linkuse as main transcript	c.369-77T>C		intron_variant			XP_011512464.1	Q68DH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMBRD2	ENST00000296603.5 linkuse as main transcript	c.369-77T>C		intron_variant		1	NM_001007527.2	ENSP00000296603.4		Q68DH5

Frequencies

GnomAD3 genomes

AF:

0.941

AC:

143231

AN:

152182

Hom.:

67792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.873

Gnomad ASJ

AF:

0.969

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.966

Gnomad FIN

AF:

0.984

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.988

Gnomad OTH

AF:

0.940

GnomAD4 exome

AF:

0.965

AC:

724074

AN:

750412

Hom.:

351302

AF XY:

0.966

AC XY:

365789

AN XY:

378618

show subpopulations

Gnomad4 AFR exome

AF:

0.899

Gnomad4 AMR exome

AF:

0.824

Gnomad4 ASJ exome

AF:

0.965

Gnomad4 EAS exome

AF:

0.682

Gnomad4 SAS exome

AF:

0.966

Gnomad4 FIN exome

AF:

0.984

Gnomad4 NFE exome

AF:

0.990

Gnomad4 OTH exome

AF:

0.958

GnomAD4 genome

AF:

0.941

AC:

143333

AN:

152300

Hom.:

67843

Cov.:

AF XY:

0.939

AC XY:

69885

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.900

Gnomad4 AMR

AF:

0.872

Gnomad4 ASJ

AF:

0.969

Gnomad4 EAS

AF:

0.713

Gnomad4 SAS

AF:

0.967

Gnomad4 FIN

AF:

0.984

Gnomad4 NFE

AF:

0.988

Gnomad4 OTH

AF:

0.940

Alfa

AF:

0.967

Hom.:

85596

Bravo

AF:

0.928

Asia WGS

AF:

0.867

AC:

3011

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.69

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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