rs17477151

Variant names:

• chr11-40185534-G-A
• rs17477151
• NM_001258419.2:c.-95-44681C>T

Variant summary

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

The NM_001258419.2(LRRC4C):​c.-95-44681C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,234 control chromosomes in the GnomAD database, including 496 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 0.070 (496 hom., cov: 32)
• Consequence: LRRC4C NM_001258419.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0975 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	NM_001258419.2	MANE Select	c.-95-44681C>T		intron	N/A	NP_001245348.1
	LRRC4C	NM_020929.3		c.-95-44681C>T		intron	N/A	NP_065980.1
	LRRC4C	NR_047673.1		n.939-44681C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC4C	ENST00000528697.6	TSL:1 MANE Select	c.-95-44681C>T		intron	N/A	ENSP00000437132.1
	LRRC4C	ENST00000278198.2	TSL:1	c.-42-69200C>T		intron	N/A	ENSP00000278198.1
	LRRC4C	ENST00000527150.5	TSL:1	c.-95-44681C>T		intron	N/A	ENSP00000436976.1

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10614 AN: 152116 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.0759

Gnomad SAS AF: 0.0897

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0697 AC: 10614 AN: 152234 Hom.: 496 Cov.: 32 AF XY: 0.0694 AC XY: 5163 AN XY: 74432

African (AFR) AF: 0.0176 AC: 731 AN: 41568

American (AMR) AF: 0.102 AC: 1553 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 198 AN: 3472

East Asian (EAS) AF: 0.0759 AC: 393 AN: 5180

South Asian (SAS) AF: 0.0902 AC: 435 AN: 4824

European-Finnish (FIN) AF: 0.0775 AC: 820 AN: 10584

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6253 AN: 68014

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0859 Hom.: 1008

Bravo AF: 0.0690

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.12
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: rs17477151; hg19: chr11-40207084;