rs10492739

Variant names:

• chr13-39388654-C-A
• rs10492739
• NM_005780.3:c.386-10128G>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.386-10128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,088 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 32)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 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.386-10128G>T		intron	N/A	NP_005771.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL6	ENST00000379589.4	TSL:1 MANE Select	c.386-10128G>T		intron	N/A	ENSP00000368908.3
	LHFPL6	ENST00000855018.1		c.479-10128G>T		intron	N/A	ENSP00000525077.1
	LHFPL6	ENST00000855017.1		c.455-10128G>T		intron	N/A	ENSP00000525076.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19543 AN: 151970 Hom.: 1322 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.129 AC: 19548 AN: 152088 Hom.: 1327 Cov.: 32 AF XY: 0.129 AC XY: 9574 AN XY: 74344

African (AFR) AF: 0.128 AC: 5289 AN: 41472

American (AMR) AF: 0.0848 AC: 1296 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3470

East Asian (EAS) AF: 0.133 AC: 686 AN: 5162

South Asian (SAS) AF: 0.203 AC: 976 AN: 4806

European-Finnish (FIN) AF: 0.109 AC: 1154 AN: 10578

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9414 AN: 67996

Other (OTH) AF: 0.124 AC: 262 AN: 2112

Alfa AF: 0.137 Hom.: 2092

Bravo AF: 0.127

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.59
PhyloP100		-0.42
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: rs10492739; hg19: chr13-39962791;