NM_005780.3:c.484+8603G>A

Variant names:

• chr13-39369825-C-T
• rs9315679
• NM_005780.3:c.484+8603G>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.484+8603G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,718 control chromosomes in the GnomAD database, including 23,654 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 0.55 (23654 hom., cov: 30)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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.484+8603G>A		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.484+8603G>A		intron	N/A	ENSP00000368908.3	Q9Y693
	LHFPL6	ENST00000855018.1		c.577+8603G>A		intron	N/A	ENSP00000525077.1
	LHFPL6	ENST00000855017.1		c.553+8603G>A		intron	N/A	ENSP00000525076.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83419 AN: 151598 Hom.: 23634 Cov.: 30

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.550 AC: 83445 AN: 151718 Hom.: 23654 Cov.: 30 AF XY: 0.554 AC XY: 41121 AN XY: 74162

African (AFR) AF: 0.399 AC: 16489 AN: 41306

American (AMR) AF: 0.605 AC: 9228 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2479 AN: 3466

East Asian (EAS) AF: 0.698 AC: 3590 AN: 5140

South Asian (SAS) AF: 0.559 AC: 2683 AN: 4802

European-Finnish (FIN) AF: 0.660 AC: 6954 AN: 10532

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40130 AN: 67918

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.563 Hom.: 9492

Bravo AF: 0.539

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.32
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: rs9315679; hg19: chr13-39943962;