chr10-71223228-G-T

Variant names:

• chr10-71223228-G-T
• rs16928529
• NM_170744.5:c.79+10164G>T

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+10164G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,012 control chromosomes in the GnomAD database, including 25,877 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 0.57 (25877 hom., cov: 32)
• Consequence: UNC5B NM_170744.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 13 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]

LOC112268061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5B	NM_170744.5	c.79+10164G>T		intron_variant	Intron 1 of 16	ENST00000335350.10	NP_734465.2
LOC112268061	XR_002957082.2	n.3621G>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC112268061	XR_002957083.2	n.3621G>T		non_coding_transcript_exon_variant	Exon 1 of 2
UNC5B	NM_001244889.2	c.79+10164G>T		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+10164G>T		intron_variant	Intron 1 of 16	1	NM_170744.5	ENSP00000334329.6
UNC5B	ENST00000373192.4	c.79+10164G>T		intron_variant	Intron 1 of 15	1		ENSP00000362288.4

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86550 AN: 151894 Hom.: 25863 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.570 AC: 86596 AN: 152012 Hom.: 25877 Cov.: 32 AF XY: 0.575 AC XY: 42693 AN XY: 74312

African (AFR) AF: 0.372 AC: 15415 AN: 41414

American (AMR) AF: 0.674 AC: 10303 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2513 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3570 AN: 5162

South Asian (SAS) AF: 0.746 AC: 3588 AN: 4810

European-Finnish (FIN) AF: 0.599 AC: 6346 AN: 10590

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42627 AN: 67970

Other (OTH) AF: 0.616 AC: 1300 AN: 2110

Alfa AF: 0.615 Hom.: 74969

Bravo AF: 0.563

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.020
DANN	Benign	0.68
PhyloP100		-3.1
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: rs16928529; hg19: chr10-72982985;