rs784420

chr5-78691701-A-G

Variant summary

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

The XR_007058832.1(LOC124900191):n.489+26383T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,188 control chromosomes in the GnomAD database, including 4,942 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 0.22 (4942 hom., cov: 32)
• Consequence: LOC124900191 XR_007058832.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

LOC124900191 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900191	XR_007058832.1	n.489+26383T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LHFPL2	ENST00000514587.1	n.402-59333T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33999 AN: 152070 Hom.: 4934 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.00866

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.224 AC: 34015 AN: 152188 Hom.: 4942 Cov.: 32 AF XY: 0.226 AC XY: 16800 AN XY: 74410

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.232

Alfa AF: 0.288 Hom.: 13113

Bravo AF: 0.222

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	12
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784420; hg19: chr5-77987524;