8-35387755-T-G

Variant names:

• chr8-35387755-T-G
• rs6468317
• NM_080872.4:c.103+151868T>G

Variant summary

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

The NM_080872.4(UNC5D):​c.103+151868T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,942 control chromosomes in the GnomAD database, including 19,631 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 0.50 (19631 hom., cov: 32)
• Consequence: UNC5D NM_080872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 2 publications found

Genes affected

UNC5D (HGNC:18634): (unc-5 netrin receptor D) Predicted to enable netrin receptor activity. Involved in cell-cell adhesion via plasma-membrane adhesion molecules. Predicted to be located in cell surface and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080872.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNC5D	NM_080872.4	MANE Select	c.103+151868T>G		intron	N/A	NP_543148.2
	UNC5D	NM_001438417.1		c.103+151868T>G		intron	N/A	NP_001425346.1
	UNC5D	NM_001438418.1		c.103+151868T>G		intron	N/A	NP_001425347.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNC5D	ENST00000404895.7	TSL:1 MANE Select	c.103+151868T>G		intron	N/A	ENSP00000385143.2
	UNC5D	ENST00000416672.5	TSL:5	c.103+151868T>G		intron	N/A	ENSP00000412652.1
	UNC5D	ENST00000420357.5	TSL:5	c.103+151868T>G		intron	N/A	ENSP00000392739.1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76633 AN: 151824 Hom.: 19621 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.505 AC: 76679 AN: 151942 Hom.: 19631 Cov.: 32 AF XY: 0.505 AC XY: 37472 AN XY: 74262

African (AFR) AF: 0.569 AC: 23570 AN: 41450

American (AMR) AF: 0.516 AC: 7873 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1584 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3631 AN: 5152

South Asian (SAS) AF: 0.502 AC: 2425 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4131 AN: 10524

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31853 AN: 67936

Other (OTH) AF: 0.522 AC: 1103 AN: 2114

Alfa AF: 0.333 Hom.: 846

Bravo AF: 0.520

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.64
PhyloP100		0.47
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: rs6468317; hg19: chr8-35245273;