rs4073894

chr7-104826517-G-A

Variant summary

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

The NM_199000.3(LHFPL3):c.683-79670G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 161,208 control chromosomes in the GnomAD database, including 2,584 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 0.17 (2369 hom., cov: 32)
  • Exomes 𝑓: 0.20 (215 hom.)
• Consequence: LHFPL3 NM_199000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

Genes affected

LHFPL3 (HGNC:6589): (LHFPL tetraspan subfamily member 3) 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. A partial gene fragment named LHFPL4 corresponds to a portion of the first exon of this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LHFPL3	NM_199000.3	c.683-79670G>A		intron_variant		ENST00000424859.7
LHFPL3	NM_001386065.1	c.683-18865G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LHFPL3	ENST00000424859.7	c.683-79670G>A		intron_variant		1	NM_199000.3	P1
	ENST00000431233.1	n.182G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25444 AN: 151678 Hom.: 2364 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

GnomAD4 exome AF: 0.197 AC: 1858 AN: 9412 Hom.: 215 Cov.: 0 AF XY: 0.202 AC XY: 939 AN XY: 4638

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.200

Gnomad4 SAS exome AF: 0.0919

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.168 AC: 25451 AN: 151796 Hom.: 2369 Cov.: 32 AF XY: 0.163 AC XY: 12126 AN XY: 74222

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0622

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.175

Alfa AF: 0.193 Hom.: 3448

Bravo AF: 0.162

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.5
Dann	Benign	0.49

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: rs4073894; hg19: chr7-104466964;