rs532238

chr13-39379190-C-A

Variant summary

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

The NM_005780.3(LHFPL6):c.386-664G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,150 control chromosomes in the GnomAD database, including 7,258 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 (7258 hom., cov: 32)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

LHFPL6 (HGNC:6586): (LHFPL tetraspan subfamily member 6) This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. This gene is fused to a high-mobility group gene in a translocation-associated lipoma. Mutations in another LHFP-like gene result in deafness in humans and mice. Alternatively spliced transcript variants have been found; however, their full-length nature is not known. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LHFPL6	NM_005780.3	c.386-664G>T		intron_variant		ENST00000379589.4
LHFPL6	XM_011534861.2	c.386-664G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LHFPL6	ENST00000379589.4	c.386-664G>T		intron_variant		1	NM_005780.3	P1
LHFPL6	ENST00000648377.1	c.386-664G>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46653 AN: 152032 Hom.: 7243 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.307 AC: 46715 AN: 152150 Hom.: 7258 Cov.: 32 AF XY: 0.302 AC XY: 22442 AN XY: 74388

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.318

Alfa AF: 0.306 Hom.: 6779

Bravo AF: 0.308

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.36

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: rs532238; hg19: chr13-39953327;