NM_001389.5:c.2356+42879G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001389.5(DSCAM):​c.2356+42879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,764 control chromosomes in the GnomAD database, including 16,916 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 0.46 ( 16916 hom., cov: 32)

Consequence

DSCAM
NM_001389.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.155

Publications

1 publications found
Variant links:
Genes affected
DSCAM (HGNC:3039): (DS cell adhesion molecule) This gene is a member of the immunoglobulin superfamily of cell adhesion molecules (Ig-CAMs), and is involved in human central and peripheral nervous system development. This gene is a candidate for Down syndrome and congenital heart disease (DSCHD). A gene encoding a similar Ig-CAM protein is located on chromosome 11. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]
DSCAM Gene-Disease associations (from GenCC):
  • autism spectrum disorder
    Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DSCAMNM_001389.5 linkc.2356+42879G>A intron_variant Intron 11 of 32 ENST00000400454.6 NP_001380.2 O60469-1
DSCAMNM_001271534.3 linkc.2356+42879G>A intron_variant Intron 11 of 32 NP_001258463.1
DSCAMNR_073202.3 linkn.2853+42879G>A intron_variant Intron 11 of 32
DSCAMXM_017028281.2 linkc.1648+42879G>A intron_variant Intron 8 of 29 XP_016883770.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DSCAMENST00000400454.6 linkc.2356+42879G>A intron_variant Intron 11 of 32 1 NM_001389.5 ENSP00000383303.1 O60469-1
DSCAMENST00000404019.2 linkc.1612+42879G>A intron_variant Intron 7 of 28 1 ENSP00000385342.2 Q8WY19
DSCAMENST00000617870.4 linkc.1861+42879G>A intron_variant Intron 8 of 29 5 ENSP00000478698.1 A0A087WUI7

Frequencies

GnomAD3 genomes
AF:
0.464
AC:
70378
AN:
151650
Hom.:
16894
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.590
Gnomad AMI
AF:
0.422
Gnomad AMR
AF:
0.387
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.268
Gnomad SAS
AF:
0.420
Gnomad FIN
AF:
0.470
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.429
Gnomad OTH
AF:
0.446
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.464
AC:
70453
AN:
151764
Hom.:
16916
Cov.:
32
AF XY:
0.462
AC XY:
34269
AN XY:
74154
show subpopulations
African (AFR)
AF:
0.589
AC:
24399
AN:
41390
American (AMR)
AF:
0.387
AC:
5901
AN:
15244
Ashkenazi Jewish (ASJ)
AF:
0.364
AC:
1263
AN:
3470
East Asian (EAS)
AF:
0.268
AC:
1385
AN:
5170
South Asian (SAS)
AF:
0.419
AC:
2016
AN:
4808
European-Finnish (FIN)
AF:
0.470
AC:
4908
AN:
10450
Middle Eastern (MID)
AF:
0.340
AC:
100
AN:
294
European-Non Finnish (NFE)
AF:
0.429
AC:
29160
AN:
67924
Other (OTH)
AF:
0.445
AC:
936
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
1932
3863
5795
7726
9658
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
636
1272
1908
2544
3180
<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:
0.411
Hom.:
5315
Bravo
AF:
0.462
Asia WGS
AF:
0.333
AC:
1160
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.3
DANN
Benign
0.53
PhyloP100
-0.15
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

Publications

Other links and lift over

dbSNP: rs2837524; hg19: chr21-41605145; API