rs341907

Variant names:

• chr5-78668202-A-C
• rs341907
• ENST00000514587.1:n.402-35834T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-78668202-A-C
• chr5-78668202-A-G
• chr5-78668202-A-T

Variant summary

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

The ENST00000514587.1(LHFPL2):​n.402-35834T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,094 control chromosomes in the GnomAD database, including 3,887 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 (3887 hom., cov: 31)
• Consequence: LHFPL2 ENST00000514587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 2 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]

LOC124900191 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900191	XR_007058832.1	n.490-7457T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHFPL2	ENST00000514587.1	n.402-35834T>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32707 AN: 151976 Hom.: 3885 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.215 AC: 32713 AN: 152094 Hom.: 3887 Cov.: 31 AF XY: 0.214 AC XY: 15913 AN XY: 74370

African (AFR) AF: 0.287 AC: 11889 AN: 41458

American (AMR) AF: 0.137 AC: 2087 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 487 AN: 3466

East Asian (EAS) AF: 0.388 AC: 2003 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4816

European-Finnish (FIN) AF: 0.196 AC: 2077 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12311 AN: 68006

Other (OTH) AF: 0.184 AC: 388 AN: 2114

Alfa AF: 0.164 Hom.: 954

Bravo AF: 0.215

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs341907; hg19: chr5-77964025;