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GeneBe

rs2458179

chr17-46257341-G-Achr17-46257341-G-C

Variant summary

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

The XM_047437205.1(LRRC37A):c.101+9182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 150,026 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.13 ( 0 hom., cov: 33)

Consequence

LRRC37A
XM_047437205.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.709
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC37AXM_047437205.1 linkuse as main transcriptc.101+9182G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.125
AC:
18798
AN:
149916
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0396
Gnomad AMI
AF:
0.260
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.00156
Gnomad SAS
AF:
0.0628
Gnomad FIN
AF:
0.0608
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.188
Gnomad OTH
AF:
0.163
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.125
AC:
18787
AN:
150026
Hom.:
0
Cov.:
33
AF XY:
0.118
AC XY:
8631
AN XY:
73354
show subpopulations
Gnomad4 AFR
AF:
0.0395
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.00156
Gnomad4 SAS
AF:
0.0629
Gnomad4 FIN
AF:
0.0608
Gnomad4 NFE
AF:
0.188
Gnomad4 OTH
AF:
0.162
Alfa
AF:
0.0491
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
4.3
Dann
Benign
0.94

Splicing

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: rs2458179; hg19: chr17-44334707; API