chr10-71242196-C-T

Variant names:

• chr10-71242196-C-T
• rs879278
• NM_170744.5:c.79+29132C>T

Variant summary

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

The NM_170744.5(UNC5B):​c.79+29132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,026 control chromosomes in the GnomAD database, including 13,271 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 0.41 (13271 hom., cov: 32)
• Consequence: UNC5B NM_170744.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5B	NM_170744.5	c.79+29132C>T		intron_variant	Intron 1 of 16	ENST00000335350.10	NP_734465.2
UNC5B	NM_001244889.2	c.79+29132C>T		intron_variant	Intron 1 of 15		NP_001231818.1
LOC112268061	XR_002957082.2	n.22589C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC112268061	XR_002957083.2	n.22589C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC5B	ENST00000335350.10	c.79+29132C>T		intron_variant	Intron 1 of 16	1	NM_170744.5	ENSP00000334329.6
UNC5B	ENST00000373192.4	c.79+29132C>T		intron_variant	Intron 1 of 15	1		ENSP00000362288.4

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62647 AN: 151908 Hom.: 13253 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.412 AC: 62710 AN: 152026 Hom.: 13271 Cov.: 32 AF XY: 0.410 AC XY: 30460 AN XY: 74314

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.387

Alfa AF: 0.407 Hom.: 2137

Bravo AF: 0.410

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.58

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: rs879278; hg19: chr10-73001953; COSMIC: COSV58981667;