18-52611760-T-C

Position:

• chr18-52611760-T-C

Variant summary

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

The NM_005215.4(DCC):​c.92-140294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,122 control chromosomes in the GnomAD database, including 5,317 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 0.25 (5317 hom., cov: 32)
• Consequence: DCC NM_005215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

DCC (HGNC:2701): (DCC netrin 1 receptor) This gene encodes a netrin 1 receptor. The transmembrane protein is a member of the immunoglobulin superfamily of cell adhesion molecules, and mediates axon guidance of neuronal growth cones towards sources of netrin 1 ligand. The cytoplasmic tail interacts with the tyrosine kinases Src and focal adhesion kinase (FAK, also known as PTK2) to mediate axon attraction. The protein partially localizes to lipid rafts, and induces apoptosis in the absence of ligand. The protein functions as a tumor suppressor, and is frequently mutated or downregulated in colorectal cancer and esophageal carcinoma. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCC	NM_005215.4	c.92-140294T>C		intron_variant		ENST00000442544.7	NP_005206.2
DCC	XM_017025568.2	c.92-140294T>C		intron_variant			XP_016881057.1
DCC	XM_017025569.2	c.92-140294T>C		intron_variant			XP_016881058.1
DCC	XM_047437311.1	c.92-140294T>C		intron_variant			XP_047293267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCC	ENST00000442544.7	c.92-140294T>C		intron_variant		1	NM_005215.4	ENSP00000389140.2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38290 AN: 152006 Hom.: 5316 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.252 AC: 38310 AN: 152122 Hom.: 5317 Cov.: 32 AF XY: 0.246 AC XY: 18325 AN XY: 74384

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.261

Alfa AF: 0.239 Hom.: 1196

Bravo AF: 0.242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.69

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: rs719953; hg19: chr18-50138130;