rs7826624

chr8-35609769-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
UNC5D	NM_080872.4	c.570+14112C>T		intron_variant		ENST00000404895.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC5D	ENST00000404895.7	c.570+14112C>T		intron_variant		1	NM_080872.4	P4

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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.339

Alfa AF: 0.262 Hom.: 7800

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

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: rs7826624; hg19: chr8-35467287;