NM_001389.5:c.509-21740T>G

Variant names:

• chr21-40390985-A-C
• rs10483066
• NM_001389.5:c.509-21740T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001389.5(DSCAM):​c.509-21740T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,246 control chromosomes in the GnomAD database, including 807 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 0.082 (807 hom., cov: 33)
• Consequence: DSCAM NM_001389.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 0 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSCAM	NM_001389.5	c.509-21740T>G		intron_variant	Intron 3 of 32	ENST00000400454.6	NP_001380.2
DSCAM	NM_001271534.3	c.509-21740T>G		intron_variant	Intron 3 of 32		NP_001258463.1
DSCAM	NR_073202.3	n.1006-21740T>G		intron_variant	Intron 3 of 32

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSCAM	ENST00000400454.6	c.509-21740T>G		intron_variant	Intron 3 of 32	1	NM_001389.5	ENSP00000383303.1

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12446 AN: 152128 Hom.: 801 Cov.: 33

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0819 AC: 12472 AN: 152246 Hom.: 807 Cov.: 33 AF XY: 0.0859 AC XY: 6390 AN XY: 74432

African (AFR) AF: 0.0623 AC: 2587 AN: 41558

American (AMR) AF: 0.236 AC: 3614 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1128 AN: 5160

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4826

European-Finnish (FIN) AF: 0.0556 AC: 590 AN: 10610

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3834 AN: 68024

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.0700 Hom.: 487

Bravo AF: 0.0986

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.41
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

Other links and lift over

dbSNP: rs10483066; hg19: chr21-41762912;