rs7928155

Variant names:

• chr11-41190552-A-G
• rs7928155
• NM_001258419.2:c.-495-256829T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-41190552-A-G
• chr11-41190552-A-T

Variant summary

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

The ENST00000528697.6(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 ENST00000528697.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528697.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	NM_001258419.2	MANE Select	c.-495-256829T>C		intron	N/A	NP_001245348.1
	LRRC4C	NM_020929.3		c.-327+268879T>C		intron	N/A	NP_065980.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	ENST00000528697.6	TSL:1 MANE Select	c.-495-256829T>C		intron	N/A	ENSP00000437132.1
	LRRC4C	ENST00000530763.5	TSL:1	c.-327+268879T>C		intron	N/A	ENSP00000434761.1
	LRRC4C	ENST00000534577.1	TSL:3	n.418+32245T>C		intron	N/A

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

African (AFR) AF: 0.136 AC: 5641 AN: 41476

American (AMR) AF: 0.403 AC: 6140 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1904 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2255 AN: 5148

South Asian (SAS) AF: 0.566 AC: 2730 AN: 4824

European-Finnish (FIN) AF: 0.638 AC: 6727 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39033 AN: 67970

Other (OTH) AF: 0.473 AC: 996 AN: 2106

Alfa AF: 0.487 Hom.: 5164

Bravo AF: 0.402

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		0.69
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: rs7928155; hg19: chr11-41212102;