rs10837366

Variant names:

• chr11-40202799-C-T
• rs10837366
• NM_001258419.2:c.-96+38720G>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.-96+38720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,826 control chromosomes in the GnomAD database, including 26,333 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 0.59 (26333 hom., cov: 31)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	NM_001258419.2	MANE Select	c.-96+38720G>A		intron	N/A	NP_001245348.1	Q9HCJ2
	LRRC4C	NM_020929.3		c.-95-61946G>A		intron	N/A	NP_065980.1	Q9HCJ2
	LRRC4C	NR_047673.1		n.939-61946G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	ENST00000528697.6	TSL:1 MANE Select	c.-96+38720G>A		intron	N/A	ENSP00000437132.1	Q9HCJ2
	LRRC4C	ENST00000278198.2	TSL:1	c.-42-86465G>A		intron	N/A	ENSP00000278198.1	Q9HCJ2
	LRRC4C	ENST00000527150.5	TSL:1	c.-95-61946G>A		intron	N/A	ENSP00000436976.1	Q9HCJ2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89097 AN: 151710 Hom.: 26315 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.587 AC: 89159 AN: 151826 Hom.: 26333 Cov.: 31 AF XY: 0.590 AC XY: 43752 AN XY: 74178

African (AFR) AF: 0.558 AC: 23085 AN: 41404

American (AMR) AF: 0.640 AC: 9759 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3843 AN: 5122

South Asian (SAS) AF: 0.537 AC: 2584 AN: 4810

European-Finnish (FIN) AF: 0.605 AC: 6370 AN: 10526

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39516 AN: 67916

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.567 Hom.: 16883

Bravo AF: 0.590

Asia WGS AF: 0.606 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.62
PhyloP100		0.57
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: rs10837366; hg19: chr11-40224349;