rs10501264

Variant names:

• chr11-41409280-C-T
• rs10501264
• NM_001258419.2:c.-496+50151G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000255132 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258419.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	NM_001258419.2	MANE Select	c.-496+50151G>A		intron	N/A	NP_001245348.1
	LRRC4C	NM_020929.3		c.-327+50151G>A		intron	N/A	NP_065980.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	ENST00000528697.6	TSL:1 MANE Select	c.-496+50151G>A		intron	N/A	ENSP00000437132.1
	LRRC4C	ENST00000530763.5	TSL:1	c.-327+50151G>A		intron	N/A	ENSP00000434761.1
	ENSG00000255132	ENST00000524493.1	TSL:4	n.255+14431C>T		intron	N/A

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

African (AFR) AF: 0.0767 AC: 3183 AN: 41494

American (AMR) AF: 0.370 AC: 5647 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1490 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1091 AN: 4800

European-Finnish (FIN) AF: 0.245 AC: 2583 AN: 10562

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21862 AN: 67968

Other (OTH) AF: 0.284 AC: 601 AN: 2114

Alfa AF: 0.281 Hom.: 1155

Bravo AF: 0.251

Asia WGS AF: 0.276 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.81
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10501264; hg19: chr11-41430830;