NM_005780.3:c.386-86989G>A

Variant names:

• chr13-39465515-C-T
• rs12873765
• NM_005780.3:c.386-86989G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005780.3(LHFPL6):​c.386-86989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,024 control chromosomes in the GnomAD database, including 3,458 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 0.16 (3458 hom., cov: 32)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHFPL6	NM_005780.3	c.386-86989G>A		intron_variant	Intron 2 of 3	ENST00000379589.4	NP_005771.1
LHFPL6	XM_011534861.2	c.386-86989G>A		intron_variant	Intron 2 of 3		XP_011533163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHFPL6	ENST00000379589.4	c.386-86989G>A		intron_variant	Intron 2 of 3	1	NM_005780.3	ENSP00000368908.3
LHFPL6	ENST00000648377.1	n.386-86989G>A		intron_variant	Intron 2 of 13			ENSP00000496801.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23700 AN: 151906 Hom.: 3452 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0458

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.156 AC: 23733 AN: 152024 Hom.: 3458 Cov.: 32 AF XY: 0.160 AC XY: 11910 AN XY: 74306

African (AFR) AF: 0.341 AC: 14146 AN: 41434

American (AMR) AF: 0.0767 AC: 1172 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2631 AN: 5130

South Asian (SAS) AF: 0.193 AC: 930 AN: 4812

European-Finnish (FIN) AF: 0.0968 AC: 1024 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0458 AC: 3117 AN: 68000

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.112 Hom.: 845

Bravo AF: 0.166

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.080
DANN	Benign	0.69
PhyloP100		-1.7
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: rs12873765; hg19: chr13-40039652;