chr13-39465515-C-T

Position:

• chr13-39465515-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• 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/exons	MANE	Protein	UniProt
LHFPL6	NM_005780.3	c.386-86989G>A		intron_variant		ENST00000379589.4	NP_005771.1
LHFPL6	XM_011534861.2	c.386-86989G>A		intron_variant			XP_011533163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHFPL6	ENST00000379589.4	c.386-86989G>A		intron_variant		1	NM_005780.3	ENSP00000368908	P1
LHFPL6	ENST00000648377.1	c.386-86989G>A		intron_variant, NMD_transcript_variant				ENSP00000496801

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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.0458

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0878 Hom.: 295

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

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: rs12873765; hg19: chr13-40039652;