chr11-41321635-C-T

Variant names:

• chr11-41321635-C-T
• rs2044541
• NM_001258419.2:c.-496+137796G>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.-496+137796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,828 control chromosomes in the GnomAD database, including 13,987 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 0.41 (13987 hom., cov: 31)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC4C	NM_001258419.2	c.-496+137796G>A		intron_variant	Intron 1 of 6	ENST00000528697.6	NP_001245348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-496+137796G>A		intron_variant	Intron 1 of 6	1	NM_001258419.2	ENSP00000437132.1
LRRC4C	ENST00000530763.5	c.-327+137796G>A		intron_variant	Intron 1 of 4	1		ENSP00000434761.1
LRRC4C	ENST00000534577.1	n.207-98627G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62673 AN: 151710 Hom.: 13976 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.413 AC: 62708 AN: 151828 Hom.: 13987 Cov.: 31 AF XY: 0.412 AC XY: 30582 AN XY: 74180

African (AFR) AF: 0.239 AC: 9904 AN: 41380

American (AMR) AF: 0.446 AC: 6811 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1788 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1804 AN: 5150

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4820

European-Finnish (FIN) AF: 0.488 AC: 5117 AN: 10494

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33645 AN: 67946

Other (OTH) AF: 0.452 AC: 951 AN: 2104

Alfa AF: 0.445 Hom.: 7651

Bravo AF: 0.406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		0.65
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: rs2044541; hg19: chr11-41343185; COSMIC: COSV73182236;