NM_016356.5:c.349-8372T>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016356.5(DCDC2):c.349-8372T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,076 control chromosomes in the GnomAD database, including 47,678 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 0.77 ( 47678 hom., cov: 32)
Consequence
DCDC2
NM_016356.5 intron
NM_016356.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.145
Publications
2 publications found
Genes affected
DCDC2 (HGNC:18141): (doublecortin domain containing 2) This gene encodes a doublecortin domain-containing family member. The doublecortin domain has been demonstrated to bind tubulin and enhance microtubule polymerization. This family member is thought to function in neuronal migration where it may affect the signaling of primary cilia. Mutations in this gene have been associated with reading disability (RD) type 2, also referred to as developmental dyslexia. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jan 2013]
DCDC2 Gene-Disease associations (from GenCC):
- ciliopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Ambry Genetics
- isolated neonatal sclerosing cholangitisInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- nephronophthisis 19Inheritance: AR Classification: STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- hearing loss, autosomal recessiveInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Senior-Boichis syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- nonsyndromic genetic hearing lossInheritance: AR Classification: LIMITED Submitted by: ClinGen
- autosomal recessive nonsyndromic hearing loss 66Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.770 AC: 116995AN: 151958Hom.: 47671 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
116995
AN:
151958
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.770 AC: 117041AN: 152076Hom.: 47678 Cov.: 32 AF XY: 0.777 AC XY: 57779AN XY: 74352 show subpopulations
GnomAD4 genome
AF:
AC:
117041
AN:
152076
Hom.:
Cov.:
32
AF XY:
AC XY:
57779
AN XY:
74352
show subpopulations
African (AFR)
AF:
AC:
19500
AN:
41410
American (AMR)
AF:
AC:
12753
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
3080
AN:
3472
East Asian (EAS)
AF:
AC:
5146
AN:
5172
South Asian (SAS)
AF:
AC:
4409
AN:
4822
European-Finnish (FIN)
AF:
AC:
10009
AN:
10602
Middle Eastern (MID)
AF:
AC:
244
AN:
294
European-Non Finnish (NFE)
AF:
AC:
59397
AN:
68000
Other (OTH)
AF:
AC:
1685
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1128
2257
3385
4514
5642
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
846
1692
2538
3384
4230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3218
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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