rs6708166

Variant names:

• chr2-30303914-G-A
• rs6708166
• ENST00000404397.5:c.130-19605G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBH	ENST00000404397.5	c.130-19605G>A		intron_variant	Intron 2 of 2	4		ENSP00000384443.1

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;