NM_003728.4:c.125-105401G>A

Variant names:

• chr4-95441032-C-T
• rs17023881
• NM_003728.4:c.125-105401G>A

Variant summary

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

The NM_003728.4(UNC5C):​c.125-105401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 150,772 control chromosomes in the GnomAD database, including 1,228 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 0.11 (1228 hom., cov: 32)
• Consequence: UNC5C NM_003728.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 2 publications found

Genes affected

UNC5C (HGNC:12569): (unc-5 netrin receptor C) This gene product belongs to the UNC-5 family of netrin receptors. Netrins are secreted proteins that direct axon extension and cell migration during neural development. They are bifunctional proteins that act as attractants for some cell types and as repellents for others, and these opposite actions are thought to be mediated by two classes of receptors. The UNC-5 family of receptors mediate the repellent response to netrin; they are transmembrane proteins containing 2 immunoglobulin (Ig)-like domains and 2 type I thrombospondin motifs in the extracellular region. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5C	NM_003728.4	c.125-105401G>A		intron_variant	Intron 1 of 15	ENST00000453304.6	NP_003719.3
UNC5C	XM_005263321.4	c.125-105401G>A		intron_variant	Intron 1 of 16		XP_005263378.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC5C	ENST00000453304.6	c.125-105401G>A		intron_variant	Intron 1 of 15	1	NM_003728.4	ENSP00000406022.1
UNC5C	ENST00000513796.5	c.125-105401G>A		intron_variant	Intron 1 of 13	1		ENSP00000426924.1
UNC5C	ENST00000506749.5	c.125-105401G>A		intron_variant	Intron 1 of 10	1		ENSP00000426153.1
UNC5C	ENST00000504962.1	c.125-105401G>A		intron_variant	Intron 1 of 5	2		ENSP00000425117.1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15843 AN: 150632 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.105 AC: 15871 AN: 150772 Hom.: 1228 Cov.: 32 AF XY: 0.103 AC XY: 7609 AN XY: 73668

African (AFR) AF: 0.210 AC: 8654 AN: 41202

American (AMR) AF: 0.0567 AC: 854 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3468

East Asian (EAS) AF: 0.161 AC: 799 AN: 4960

South Asian (SAS) AF: 0.122 AC: 558 AN: 4560

European-Finnish (FIN) AF: 0.0598 AC: 629 AN: 10514

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0595 AC: 4025 AN: 67692

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0732 Hom.: 1766

Bravo AF: 0.107

Asia WGS AF: 0.148 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		0.022
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: rs17023881; hg19: chr4-96362183;