rs7826624

Variant names:

• chr8-35609769-C-T
• rs7826624
• NM_080872.4:c.570+14112C>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+14112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,062 control chromosomes in the GnomAD database, including 12,523 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 0.36 (12523 hom., cov: 32)
• Consequence: UNC5D NM_080872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UNC5D	NM_080872.4	c.570+14112C>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+14112C>T		intron_variant	Intron 4 of 16	1	NM_080872.4	ENSP00000385143.2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54836 AN: 151944 Hom.: 12511 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.361 AC: 54876 AN: 152062 Hom.: 12523 Cov.: 32 AF XY: 0.355 AC XY: 26375 AN XY: 74316

African (AFR) AF: 0.652 AC: 27055 AN: 41472

American (AMR) AF: 0.335 AC: 5113 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1654 AN: 5148

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15929 AN: 67986

Other (OTH) AF: 0.339 AC: 717 AN: 2114

Alfa AF: 0.275 Hom.: 11193

Bravo AF: 0.389

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.065
DANN	Benign	0.33
PhyloP100		-3.2
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: rs7826624; hg19: chr8-35467287;