rs1371671

Variant summary

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

The NM_001258419.2(LRRC4C):​c.-269-102299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,130 control chromosomes in the GnomAD database, including 11,564 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 0.38 ( 11564 hom., cov: 33)

Consequence

LRRC4C
NM_001258419.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40
Variant links:
Genes affected
LRRC4C (HGNC:29317): (leucine rich repeat containing 4C) NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]

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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC4CNM_001258419.2 linkuse as main transcriptc.-269-102299G>A intron_variant ENST00000528697.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRRC4CENST00000528697.6 linkuse as main transcriptc.-269-102299G>A intron_variant 1 NM_001258419.2 P1
LRRC4CENST00000530763.5 linkuse as main transcriptc.-189-102299G>A intron_variant 1 P1

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
58454
AN:
152012
Hom.:
11563
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.315
Gnomad AMI
AF:
0.430
Gnomad AMR
AF:
0.400
Gnomad ASJ
AF:
0.409
Gnomad EAS
AF:
0.454
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.478
Gnomad MID
AF:
0.401
Gnomad NFE
AF:
0.396
Gnomad OTH
AF:
0.391
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.384
AC:
58474
AN:
152130
Hom.:
11564
Cov.:
33
AF XY:
0.387
AC XY:
28811
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.314
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.409
Gnomad4 EAS
AF:
0.454
Gnomad4 SAS
AF:
0.467
Gnomad4 FIN
AF:
0.478
Gnomad4 NFE
AF:
0.396
Gnomad4 OTH
AF:
0.392
Alfa
AF:
0.394
Hom.:
2486
Bravo
AF:
0.379
Asia WGS
AF:
0.424
AC:
1476
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.24
DANN
Benign
0.69

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: rs1371671; hg19: chr11-40443570; API