rs692713

chr5-176826434-G-Achr5-176826434-G-Cchr5-176826434-G-T

Variant summary

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

The NM_133369.3(UNC5A):c.70+15614G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,186 control chromosomes in the GnomAD database, including 49,121 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 0.74 (49121 hom., cov: 32)
• Consequence: UNC5A NM_133369.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

UNC5A (HGNC:12567): (unc-5 netrin receptor A) UNC5A belongs to a family of netrin-1 (MIM 601614) receptors thought to mediate the chemorepulsive effect of netrin-1 on specific axons. For more information on UNC5 proteins, see UNC5C (MIM 603610).[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC5A	NM_133369.3	c.70+15614G>A		intron_variant		ENST00000329542.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC5A	ENST00000329542.9	c.70+15614G>A		intron_variant		1	NM_133369.3
UNC5A	ENST00000509580.2	c.70+15614G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112556 AN: 152068 Hom.: 49123 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.740 AC: 112561 AN: 152186 Hom.: 49121 Cov.: 32 AF XY: 0.749 AC XY: 55711 AN XY: 74412

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.774

Alfa AF: 0.777 Hom.: 11805

Bravo AF: 0.702

Asia WGS AF: 0.850 AC: 2954 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	6.9
Dann	Benign	0.92

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: rs692713; hg19: chr5-176253435;