NM_005780.3:c.385+90851G>A

Variant names:

• chr13-39509981-C-T
• rs9285134
• NM_005780.3:c.385+90851G>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.385+90851G>A 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 151,998 control chromosomes in the GnomAD database, including 5,632 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 (5632 hom., cov: 33)
• Consequence: LHFPL6 NM_005780.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• 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]

LOC105370170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL6	NM_005780.3	MANE Select	c.385+90851G>A		intron	N/A	NP_005771.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL6	ENST00000379589.4	TSL:1 MANE Select	c.385+90851G>A		intron	N/A	ENSP00000368908.3
	LHFPL6	ENST00000648377.1		n.385+90851G>A		intron	N/A	ENSP00000496801.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38593 AN: 151880 Hom.: 5626 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38640 AN: 151998 Hom.: 5632 Cov.: 33 AF XY: 0.254 AC XY: 18854 AN XY: 74300

African (AFR) AF: 0.407 AC: 16852 AN: 41452

American (AMR) AF: 0.231 AC: 3529 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.189 AC: 978 AN: 5162

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4812

European-Finnish (FIN) AF: 0.157 AC: 1658 AN: 10552

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13025 AN: 67962

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.224 Hom.: 550

Bravo AF: 0.265

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.55
PhyloP100		-0.58
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: rs9285134; hg19: chr13-40084118;