rs9315695

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005780.3(LHFPL6):​c.385+90636T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,968 control chromosomes in the GnomAD database, including 5,593 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 0.25 ( 5593 hom., cov: 33)

Consequence

LHFPL6
NM_005780.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291
Variant links:
Genes affected
LHFPL6 (HGNC:6586): (LHFPL tetraspan subfamily member 6) 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. This gene is fused to a high-mobility group gene in a translocation-associated lipoma. Mutations in another LHFP-like gene result in deafness in humans and mice. Alternatively spliced transcript variants have been found; however, their full-length nature is not known. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LHFPL6NM_005780.3 linkuse as main transcriptc.385+90636T>G intron_variant ENST00000379589.4
LOC105370170XR_007063765.1 linkuse as main transcriptn.482+730A>C intron_variant, non_coding_transcript_variant
LHFPL6XM_011534861.2 linkuse as main transcriptc.385+90636T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LHFPL6ENST00000379589.4 linkuse as main transcriptc.385+90636T>G intron_variant 1 NM_005780.3 P1
LHFPL6ENST00000648377.1 linkuse as main transcriptc.385+90636T>G intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38496
AN:
151850
Hom.:
5587
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.406
Gnomad AMI
AF:
0.215
Gnomad AMR
AF:
0.231
Gnomad ASJ
AF:
0.153
Gnomad EAS
AF:
0.190
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.274
Gnomad NFE
AF:
0.192
Gnomad OTH
AF:
0.252
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38535
AN:
151968
Hom.:
5593
Cov.:
33
AF XY:
0.253
AC XY:
18794
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.406
Gnomad4 AMR
AF:
0.232
Gnomad4 ASJ
AF:
0.153
Gnomad4 EAS
AF:
0.190
Gnomad4 SAS
AF:
0.256
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.192
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.203
Hom.:
6909
Bravo
AF:
0.264
Asia WGS
AF:
0.263
AC:
916
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.3
DANN
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9315695; hg19: chr13-40084333; API