chr8-35622836-G-T

Variant names:

• chr8-35622836-G-T
• rs1439162
• NM_080872.4:c.570+27179G>T

Variant summary

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

The NM_080872.4(UNC5D):​c.570+27179G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,114 control chromosomes in the GnomAD database, including 1,128 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 0.12 (1128 hom., cov: 32)
• Consequence: UNC5D NM_080872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5D	NM_080872.4	c.570+27179G>T		intron_variant	Intron 4 of 16	ENST00000404895.7	NP_543148.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UNC5D	ENST00000404895.7	c.570+27179G>T		intron_variant	Intron 4 of 16	1	NM_080872.4	ENSP00000385143.2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17624 AN: 151996 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.116 AC: 17669 AN: 152114 Hom.: 1128 Cov.: 32 AF XY: 0.115 AC XY: 8551 AN XY: 74376

African (AFR) AF: 0.171 AC: 7102 AN: 41474

American (AMR) AF: 0.0726 AC: 1110 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3470

East Asian (EAS) AF: 0.0446 AC: 231 AN: 5178

South Asian (SAS) AF: 0.0750 AC: 361 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10580

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7156 AN: 68000

Other (OTH) AF: 0.104 AC: 219 AN: 2112

Alfa AF: 0.0462 Hom.: 36

Bravo AF: 0.113

Asia WGS AF: 0.0730 AC: 255 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	0.95
DANN	Benign	0.22
PhyloP100		1.5
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: rs1439162; hg19: chr8-35480354;