chr11-40917516-C-A

Variant names:

• chr11-40917516-C-A
• rs1038891
• NM_001258419.2:c.-407+16119G>T

Variant summary

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

The NM_001258419.2(LRRC4C):​c.-407+16119G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,990 control chromosomes in the GnomAD database, including 1,597 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 0.12 (1597 hom., cov: 32)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC4C	NM_001258419.2	c.-407+16119G>T		intron_variant	Intron 2 of 6	ENST00000528697.6	NP_001245348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-407+16119G>T		intron_variant	Intron 2 of 6	1	NM_001258419.2	ENSP00000437132.1
LRRC4C	ENST00000530763.5	c.-326-269238G>T		intron_variant	Intron 1 of 4	1		ENSP00000434761.1
LRRC4C	ENST00000534577.1	n.507+16119G>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17628 AN: 151870 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.116 AC: 17693 AN: 151990 Hom.: 1597 Cov.: 32 AF XY: 0.118 AC XY: 8803 AN XY: 74292

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0532 Hom.: 89

Bravo AF: 0.132

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.53

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: rs1038891; hg19: chr11-40939066;