rs532238

Variant names:

• chr13-39379190-C-A
• rs532238
• NM_005780.3:c.386-664G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005780.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL6	NM_005780.3	MANE Select	c.386-664G>T		intron	N/A	NP_005771.1	Q9Y693

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL6	ENST00000379589.4	TSL:1 MANE Select	c.386-664G>T		intron	N/A	ENSP00000368908.3	Q9Y693
	LHFPL6	ENST00000855018.1		c.479-664G>T		intron	N/A	ENSP00000525077.1
	LHFPL6	ENST00000855017.1		c.455-664G>T		intron	N/A	ENSP00000525076.1

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

African (AFR) AF: 0.343 AC: 14239 AN: 41488

American (AMR) AF: 0.258 AC: 3942 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1427 AN: 5180

South Asian (SAS) AF: 0.190 AC: 914 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10584

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21054 AN: 68004

Other (OTH) AF: 0.318 AC: 673 AN: 2114

Alfa AF: 0.311 Hom.: 17579

Bravo AF: 0.308

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.36
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs532238; hg19: chr13-39953327;