rs546447428

Variant names:

• chr10-71213056-G-A
• NM_170744.5:c.71G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-71213056-G-A
• chr10-71213056-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_170744.5(UNC5B):​c.71G>A​(p.Ser24Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000801 in 1,248,002 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.0e-7 (0 hom.)
• Consequence: UNC5B NM_170744.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.64

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14904824).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5B	NM_170744.5	c.71G>A	p.Ser24Asn	missense_variant	Exon 1 of 17	ENST00000335350.10	NP_734465.2
UNC5B	NM_001244889.2	c.71G>A	p.Ser24Asn	missense_variant	Exon 1 of 16		NP_001231818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC5B	ENST00000335350.10	c.71G>A	p.Ser24Asn	missense_variant	Exon 1 of 17	1	NM_170744.5	ENSP00000334329.6
UNC5B	ENST00000373192.4	c.71G>A	p.Ser24Asn	missense_variant	Exon 1 of 16	1		ENSP00000362288.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.01e-7 AC: 1 AN: 1248002 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 612562

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.98e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.078	T;.
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.083
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.51	T;T
M_CAP	Uncertain	0.099	D
MetaRNN	Benign	0.15	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N;N
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-0.74	N;N
REVEL	Benign	0.063
Sift	Benign	0.062	T;T
Sift4G	Benign	0.30	T;T
Polyphen		0.28	B;B
Vest4		0.27
MutPred		0.22		Loss of phosphorylation at S24 (P = 0.0384);Loss of phosphorylation at S24 (P = 0.0384);
MVP		0.59
MPC		0.17
ClinPred		0.62	D
GERP RS		3.5
Varity_R		0.079
gMVP		0.27

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-72972813;