rs10501264

Positions:

• chr11-41409280-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258419.2(LRRC4C):​c.-496+50151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,056 control chromosomes in the GnomAD database, including 5,828 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 (5828 hom., cov: 32)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC4C	NM_001258419.2	c.-496+50151G>A		intron_variant		ENST00000528697.6	NP_001245348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-496+50151G>A		intron_variant		1	NM_001258419.2	ENSP00000437132	P1
LRRC4C	ENST00000530763.5	c.-327+50151G>A		intron_variant		1		ENSP00000434761	P1
	ENST00000524493.1	n.255+14431C>T		intron_variant, non_coding_transcript_variant		4
LRRC4C	ENST00000534577.1	n.206+50151G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38011 AN: 151938 Hom.: 5823 Cov.: 32

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.250 AC: 38026 AN: 152056 Hom.: 5828 Cov.: 32 AF XY: 0.249 AC XY: 18532 AN XY: 74328

Gnomad4 AFR AF: 0.0767

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.284

Alfa AF: 0.287 Hom.: 1151

Bravo AF: 0.251

Asia WGS AF: 0.276 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs10501264; hg19: chr11-41430830;