rs6708166

chr2-30303914-G-A

Variant summary

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

The ENST00000404397.5(LBH):c.130-19605G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,698 control chromosomes in the GnomAD database, including 8,073 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 (8073 hom., cov: 30)
• Consequence: LBH ENST00000404397.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

LBH (HGNC:29532): (LBH regulator of WNT signaling pathway) Involved in negative regulation of transcription, DNA-templated; positive regulation of transcription, DNA-templated; and regulation of MAPK cascade. Located in cytoplasm and nucleus. Part of protein-containing complex. [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 = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LBH	ENST00000404397.5	c.130-19605G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47707 AN: 151578 Hom.: 8071 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.315 AC: 47733 AN: 151698 Hom.: 8073 Cov.: 30 AF XY: 0.309 AC XY: 22877 AN XY: 74136

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.345

Alfa AF: 0.361 Hom.: 14296

Bravo AF: 0.309

Asia WGS AF: 0.168 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.23
Dann	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6708166; hg19: chr2-30526780;