rs4611189

Positions:

• chr11-40816163-G-A

Variant summary

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

The NM_001258419.2(LRRC4C):​c.-407+117472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,232 control chromosomes in the GnomAD database, including 181 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 0.035 (181 hom., cov: 32)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC4C	NM_001258419.2	c.-407+117472C>T		intron_variant		ENST00000528697.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-407+117472C>T		intron_variant		1	NM_001258419.2	P1
LRRC4C	ENST00000530763.5	c.-326-167885C>T		intron_variant		1		P1
LRRC4C	ENST00000534577.1	n.507+117472C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5247 AN: 152114 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0346 AC: 5267 AN: 152232 Hom.: 181 Cov.: 32 AF XY: 0.0337 AC XY: 2508 AN XY: 74432

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.0242

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.00631

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0166 Hom.: 61

Bravo AF: 0.0362

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.56

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: rs4611189; hg19: chr11-40837713;