rs7928155

chr11-41190552-A-Gchr11-41190552-A-T

Variant summary

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

The NM_001258419.2(LRRC4C):c.-495-256829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,994 control chromosomes in the GnomAD database, including 17,405 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 0.43 (17405 hom., cov: 31)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC4C	NM_001258419.2	c.-495-256829T>C		intron_variant		ENST00000528697.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-495-256829T>C		intron_variant		1	NM_001258419.2	P1
LRRC4C	ENST00000530763.5	c.-327+268879T>C		intron_variant		1		P1
LRRC4C	ENST00000534577.1	n.418+32245T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66051 AN: 151876 Hom.: 17404 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.435 AC: 66049 AN: 151994 Hom.: 17405 Cov.: 31 AF XY: 0.438 AC XY: 32547 AN XY: 74270

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.473

Alfa AF: 0.494 Hom.: 5152

Bravo AF: 0.402

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.7
Dann	Benign	0.48

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: rs7928155; hg19: chr11-41212102;