Menu
GeneBe

rs6677080

Variant summary

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

The NM_144620.4(LRRC39):c.113+491A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,656 control chromosomes in the GnomAD database, including 4,362 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 0.20 ( 4362 hom., cov: 31)

Consequence

LRRC39
NM_144620.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310
Variant links:
Genes affected
LRRC39 (HGNC:28228): (leucine rich repeat containing 39) Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Predicted to be located in M band. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC39NM_144620.4 linkuse as main transcriptc.113+491A>T intron_variant ENST00000370137.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRRC39ENST00000370137.6 linkuse as main transcriptc.113+491A>T intron_variant 1 NM_144620.4 P1Q96DD0-1
LRRC39ENST00000342895.8 linkuse as main transcriptc.113+491A>T intron_variant 5 P1Q96DD0-1
LRRC39ENST00000370138.1 linkuse as main transcriptc.113+491A>T intron_variant 5 Q96DD0-2

Frequencies

GnomAD3 genomes
AF:
0.200
AC:
30335
AN:
151548
Hom.:
4344
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.405
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.120
Gnomad ASJ
AF:
0.102
Gnomad EAS
AF:
0.0485
Gnomad SAS
AF:
0.0985
Gnomad FIN
AF:
0.0906
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.200
AC:
30394
AN:
151656
Hom.:
4362
Cov.:
31
AF XY:
0.195
AC XY:
14478
AN XY:
74150
show subpopulations
Gnomad4 AFR
AF:
0.406
Gnomad4 AMR
AF:
0.120
Gnomad4 ASJ
AF:
0.102
Gnomad4 EAS
AF:
0.0488
Gnomad4 SAS
AF:
0.0990
Gnomad4 FIN
AF:
0.0906
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.173
Alfa
AF:
0.175
Hom.:
374
Bravo
AF:
0.210
Asia WGS
AF:
0.113
AC:
391
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.92
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

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

Other links and lift over

dbSNP: rs6677080; hg19: chr1-100633469; API