rs6563695

Positions:

• chr13-39329106-G-T

Variant summary

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

The ENST00000648377.1(LHFPL6):​n.*82+14748C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,170 control chromosomes in the GnomAD database, including 1,476 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 0.12 (1476 hom., cov: 32)
• Consequence: LHFPL6 ENST00000648377.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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]

LOC107984580 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984580	XR_001749845.1	n.1449+7165C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHFPL6	ENST00000648377.1	n.*82+14748C>A		intron_variant				ENSP00000496801.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18308 AN: 152052 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.120 AC: 18324 AN: 152170 Hom.: 1476 Cov.: 32 AF XY: 0.124 AC XY: 9193 AN XY: 74382

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0858 Hom.: 392

Bravo AF: 0.125

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6563695; hg19: chr13-39903243;