chr5-78614116-C-T

Variant names:

• chr5-78614116-C-T
• rs1372319
• NM_005779.3:c.-245+18148G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005779.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL2	NM_005779.3	MANE Select	c.-245+18148G>A		intron	N/A	NP_005770.1	Q6ZUX7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LHFPL2	ENST00000380345.7	TSL:5 MANE Select	c.-245+18148G>A		intron	N/A	ENSP00000369702.2	Q6ZUX7
	LHFPL2	ENST00000872133.1		c.-245+18148G>A		intron	N/A	ENSP00000542192.1
	LHFPL2	ENST00000872134.1		c.-422-9347G>A		intron	N/A	ENSP00000542193.1

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

African (AFR) AF: 0.580 AC: 24030 AN: 41462

American (AMR) AF: 0.650 AC: 9944 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2231 AN: 3464

East Asian (EAS) AF: 0.504 AC: 2604 AN: 5170

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4816

European-Finnish (FIN) AF: 0.732 AC: 7748 AN: 10588

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47992 AN: 67950

Other (OTH) AF: 0.646 AC: 1365 AN: 2114

Alfa AF: 0.684 Hom.: 58613

Bravo AF: 0.646

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.73
PhyloP100		-0.42
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: rs1372319; hg19: chr5-77909939;