5-36147704-C-T

Position:

• chr5-36147704-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007527.2(LMBRD2):​c.-58+3852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,006 control chromosomes in the GnomAD database, including 8,126 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 0.31 (8126 hom., cov: 32)
• Consequence: LMBRD2 NM_001007527.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMBRD2	NM_001007527.2	c.-58+3852G>A		intron_variant		ENST00000296603.5
LMBRD2	XM_011514162.3	c.-58+3384G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMBRD2	ENST00000296603.5	c.-58+3852G>A		intron_variant		1	NM_001007527.2	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47138 AN: 151888 Hom.: 8133 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.310 AC: 47138 AN: 152006 Hom.: 8126 Cov.: 32 AF XY: 0.309 AC XY: 22937 AN XY: 74278

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.326

Alfa AF: 0.336 Hom.: 3920

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs10071838; hg19: chr5-36147806;