rs11760238

Variant names:

• chr7-104483097-G-A
• rs11760238
• NM_199000.3:c.445+153873G>A

Variant summary

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

The NM_199000.3(LHFPL3):​c.445+153873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,052 control chromosomes in the GnomAD database, including 11,956 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 0.38 (11956 hom., cov: 33)
• Consequence: LHFPL3 NM_199000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.924
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHFPL3	NM_199000.3	c.445+153873G>A		intron_variant	Intron 1 of 2	ENST00000424859.7	NP_945351.1
LHFPL3	NM_001386065.1	c.445+153873G>A		intron_variant	Intron 1 of 3		NP_001372994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHFPL3	ENST00000424859.7	c.445+153873G>A		intron_variant	Intron 1 of 2	1	NM_199000.3	ENSP00000393128.2
LHFPL3	ENST00000401970.3	c.445+153873G>A		intron_variant	Intron 1 of 3	1		ENSP00000385374.3
LHFPL3	ENST00000683240.1	n.*52+84912G>A		intron_variant	Intron 2 of 3			ENSP00000508253.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57790 AN: 151934 Hom.: 11961 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.380 AC: 57806 AN: 152052 Hom.: 11956 Cov.: 33 AF XY: 0.372 AC XY: 27651 AN XY: 74308

African (AFR) AF: 0.238 AC: 9880 AN: 41478

American (AMR) AF: 0.351 AC: 5369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3466

East Asian (EAS) AF: 0.202 AC: 1047 AN: 5176

South Asian (SAS) AF: 0.314 AC: 1517 AN: 4828

European-Finnish (FIN) AF: 0.381 AC: 4020 AN: 10560

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32878 AN: 67962

Other (OTH) AF: 0.410 AC: 861 AN: 2102

Alfa AF: 0.449 Hom.: 69440

Bravo AF: 0.370

Asia WGS AF: 0.245 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.92
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: rs11760238; hg19: chr7-104123545;