rs10823706

chr10-71249100-A-Cchr10-71249100-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_170744.5(UNC5B):c.80-30721A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,054 control chromosomes in the GnomAD database, including 13,724 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 0.42 (13724 hom., cov: 32)
• Consequence: UNC5B NM_170744.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

UNC5B (HGNC:12568): (unc-5 netrin receptor B) This gene encodes a member of the netrin family of receptors. This particular protein mediates the repulsive effect of netrin-1 and is a vascular netrin receptor. This encoded protein is also in a group of proteins called dependence receptors (DpRs) which are involved in pro- and anti-apoptotic processes. Many DpRs are involved in embryogenesis and in cancer progression. Two alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2011]

LOC112268061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC5B	NM_170744.5	c.80-30721A>C		intron_variant		ENST00000335350.10
LOC112268061	XR_002957082.2	n.27961A>C		non_coding_transcript_exon_variant	2/2
UNC5B	NM_001244889.2	c.80-30721A>C		intron_variant
LOC112268061	XR_002957083.2	n.27780A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC5B	ENST00000335350.10	c.80-30721A>C		intron_variant		1	NM_170744.5	P4
UNC5B	ENST00000373192.4	c.80-30721A>C		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63229 AN: 151936 Hom.: 13733 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.416 AC: 63238 AN: 152054 Hom.: 13724 Cov.: 32 AF XY: 0.415 AC XY: 30849 AN XY: 74302

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.445

Alfa AF: 0.459 Hom.: 21357

Bravo AF: 0.402

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.035
Dann	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs10823706; hg19: chr10-73008857;