5-78614116-C-T

Position:

• chr5-78614116-C-T

Variant summary

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

The NM_005779.3(LHFPL2):​c.-245+18148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,062 control chromosomes in the GnomAD database, including 32,497 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 0.65 (32497 hom., cov: 33)
• Consequence: LHFPL2 NM_005779.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

LHFPL2 (HGNC:6588): (LHFPL tetraspan subfamily member 2) 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. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. Alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

LHFPL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LHFPL2	NM_005779.3	c.-245+18148G>A		intron_variant		ENST00000380345.7	NP_005770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHFPL2	ENST00000380345.7	c.-245+18148G>A		intron_variant		5	NM_005779.3	ENSP00000369702.2
LHFPL2	ENST00000503686.5	n.119+34383G>A		intron_variant		4
LHFPL2	ENST00000512759.5	n.502+18148G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98928 AN: 151944 Hom.: 32481 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.651 AC: 98992 AN: 152062 Hom.: 32497 Cov.: 33 AF XY: 0.647 AC XY: 48062 AN XY: 74332

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.646

Alfa AF: 0.689 Hom.: 46729

Bravo AF: 0.646

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.73

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: rs1372319; hg19: chr5-77909939;