rs9315695

Variant names:

• chr13-39510196-A-C
• rs9315695
• NM_005780.3:c.385+90636T>G

Variant summary

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

The NM_005780.3(LHFPL6):​c.385+90636T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,968 control chromosomes in the GnomAD database, including 5,593 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 0.25 (5593 hom., cov: 33)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 4 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]

LOC105370170 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHFPL6	NM_005780.3	c.385+90636T>G		intron_variant	Intron 2 of 3	ENST00000379589.4	NP_005771.1
LHFPL6	XM_011534861.2	c.385+90636T>G		intron_variant	Intron 2 of 3		XP_011533163.1
LOC105370170	XR_007063765.1	n.482+730A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHFPL6	ENST00000379589.4	c.385+90636T>G		intron_variant	Intron 2 of 3	1	NM_005780.3	ENSP00000368908.3
LHFPL6	ENST00000648377.1	n.385+90636T>G		intron_variant	Intron 2 of 13			ENSP00000496801.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38496 AN: 151850 Hom.: 5587 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.254 AC: 38535 AN: 151968 Hom.: 5593 Cov.: 33 AF XY: 0.253 AC XY: 18794 AN XY: 74276

African (AFR) AF: 0.406 AC: 16770 AN: 41352

American (AMR) AF: 0.232 AC: 3536 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3470

East Asian (EAS) AF: 0.190 AC: 981 AN: 5160

South Asian (SAS) AF: 0.256 AC: 1231 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1649 AN: 10588

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13031 AN: 68002

Other (OTH) AF: 0.253 AC: 533 AN: 2110

Alfa AF: 0.212 Hom.: 16578

Bravo AF: 0.264

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9315695; hg19: chr13-40084333;