chr7-104420525-G-A

Position:

• chr7-104420525-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.445+91301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,600 control chromosomes in the GnomAD database, including 1,023 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 0.11 (1023 hom., cov: 32)
• Consequence: LHFPL3 NM_199000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LHFPL3	NM_199000.3	c.445+91301G>A		intron_variant		ENST00000424859.7	NP_945351.1
LHFPL3	NM_001386065.1	c.445+91301G>A		intron_variant			NP_001372994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHFPL3	ENST00000424859.7	c.445+91301G>A		intron_variant		1	NM_199000.3	ENSP00000393128	P1
LHFPL3	ENST00000401970.3	c.445+91301G>A		intron_variant		1		ENSP00000385374
LHFPL3	ENST00000683240.1	c.*52+22340G>A		intron_variant, NMD_transcript_variant				ENSP00000508253

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16157 AN: 151490 Hom.: 1023 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.107 AC: 16165 AN: 151600 Hom.: 1023 Cov.: 32 AF XY: 0.106 AC XY: 7874 AN XY: 74064

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.0889

Gnomad4 FIN AF: 0.0635

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0909 Hom.: 1144

Bravo AF: 0.107

Asia WGS AF: 0.169 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.063
DANN	Benign	0.71

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: rs6976167; hg19: chr7-104060973;