11-40246547-C-T

Variant names:

• chr11-40246547-C-T
• rs7125624
• NM_001258419.2:c.-175-4949G>A

Variant summary

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

The NM_001258419.2(LRRC4C):​c.-175-4949G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,964 control chromosomes in the GnomAD database, including 46,214 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 0.75 (46214 hom., cov: 31)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC4C	NM_001258419.2	c.-175-4949G>A		intron_variant	Intron 4 of 6	ENST00000528697.6	NP_001245348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-175-4949G>A		intron_variant	Intron 4 of 6	1	NM_001258419.2	ENSP00000437132.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113358 AN: 151846 Hom.: 46215 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.746 AC: 113384 AN: 151964 Hom.: 46214 Cov.: 31 AF XY: 0.750 AC XY: 55677 AN XY: 74282

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.793

Alfa AF: 0.856 Hom.: 21783

Bravo AF: 0.730

Asia WGS AF: 0.878 AC: 3051 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.075
DANN	Benign	0.61

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: rs7125624; hg19: chr11-40268097;