rs1367634

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005215.4(DCC):​c.2165-1415T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,076 control chromosomes in the GnomAD database, including 29,857 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 0.62 ( 29857 hom., cov: 33)

Consequence

DCC
NM_005215.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DCCNM_005215.4 linkuse as main transcriptc.2165-1415T>G intron_variant ENST00000442544.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DCCENST00000442544.7 linkuse as main transcriptc.2165-1415T>G intron_variant 1 NM_005215.4 P1
DCCENST00000581580.5 linkuse as main transcriptc.1130-1415T>G intron_variant 1
DCCENST00000304775.12 linkuse as main transcriptc.1966-1415T>G intron_variant, NMD_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94301
AN:
151956
Hom.:
29820
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.678
Gnomad AMI
AF:
0.617
Gnomad AMR
AF:
0.489
Gnomad ASJ
AF:
0.536
Gnomad EAS
AF:
0.417
Gnomad SAS
AF:
0.435
Gnomad FIN
AF:
0.662
Gnomad MID
AF:
0.605
Gnomad NFE
AF:
0.641
Gnomad OTH
AF:
0.628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.621
AC:
94384
AN:
152076
Hom.:
29857
Cov.:
33
AF XY:
0.615
AC XY:
45705
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.679
Gnomad4 AMR
AF:
0.488
Gnomad4 ASJ
AF:
0.536
Gnomad4 EAS
AF:
0.417
Gnomad4 SAS
AF:
0.436
Gnomad4 FIN
AF:
0.662
Gnomad4 NFE
AF:
0.641
Gnomad4 OTH
AF:
0.625
Alfa
AF:
0.628
Hom.:
49125
Bravo
AF:
0.609
Asia WGS
AF:
0.465
AC:
1618
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.20
DANN
Benign
0.59

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1367634; hg19: chr18-50864668; API