rs7924805

Variant names:

• chr11-40189702-T-C
• rs7924805
• NM_001258419.2:c.-95-48849A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258419.2(LRRC4C):​c.-95-48849A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,066 control chromosomes in the GnomAD database, including 28,475 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 0.61 (28475 hom., cov: 33)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC4C	NM_001258419.2	c.-95-48849A>G		intron_variant	Intron 5 of 6	ENST00000528697.6	NP_001245348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC4C	ENST00000528697.6	c.-95-48849A>G		intron_variant	Intron 5 of 6	1	NM_001258419.2	ENSP00000437132.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92409 AN: 151948 Hom.: 28446 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.608 AC: 92486 AN: 152066 Hom.: 28475 Cov.: 33 AF XY: 0.613 AC XY: 45577 AN XY: 74336

African (AFR) AF: 0.687 AC: 28496 AN: 41488

American (AMR) AF: 0.611 AC: 9340 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2940 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.622 AC: 6570 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37579 AN: 67966

Other (OTH) AF: 0.571 AC: 1202 AN: 2106

Alfa AF: 0.568 Hom.: 103906

Bravo AF: 0.603

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.35
PhyloP100		-0.77
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: rs7924805; hg19: chr11-40211252;