10-71215171-T-G

Variant names:

• chr10-71215171-T-G
• rs10762430
• NM_170744.5:c.79+2107T>G

Variant summary

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

The NM_170744.5(UNC5B):​c.79+2107T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,142 control chromosomes in the GnomAD database, including 14,334 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 (14334 hom., cov: 32)
• Consequence: UNC5B NM_170744.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 1 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5B	NM_170744.5	c.79+2107T>G		intron_variant	Intron 1 of 16	ENST00000335350.10	NP_734465.2
UNC5B	NM_001244889.2	c.79+2107T>G		intron_variant	Intron 1 of 15		NP_001231818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC5B	ENST00000335350.10	c.79+2107T>G		intron_variant	Intron 1 of 16	1	NM_170744.5	ENSP00000334329.6
UNC5B	ENST00000373192.4	c.79+2107T>G		intron_variant	Intron 1 of 15	1		ENSP00000362288.4

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65172 AN: 152024 Hom.: 14302 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.429 AC: 65248 AN: 152142 Hom.: 14334 Cov.: 32 AF XY: 0.430 AC XY: 31975 AN XY: 74370

African (AFR) AF: 0.484 AC: 20093 AN: 41496

American (AMR) AF: 0.344 AC: 5269 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1268 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3068 AN: 5152

South Asian (SAS) AF: 0.400 AC: 1931 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4735 AN: 10598

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27599 AN: 67986

Other (OTH) AF: 0.432 AC: 913 AN: 2114

Alfa AF: 0.412 Hom.: 19198

Bravo AF: 0.428

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.2
DANN	Benign	0.85
PhyloP100		-0.54
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: rs10762430; hg19: chr10-72974928;