chr21-40042669-T-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001389.5(DSCAM):c.5388A>C(p.Arg1796=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000779 in 1,271,104 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00075 ( 4 hom. )
Consequence
DSCAM
NM_001389.5 synonymous
NM_001389.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.122
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 21-40042669-T-G is Benign according to our data. Variant chr21-40042669-T-G is described in ClinVar as [Benign]. Clinvar id is 742975.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.122 with no splicing effect.
BS2
?
High AC in GnomAd at 78 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSCAM | NM_001389.5 | c.5388A>C | p.Arg1796= | synonymous_variant | 32/33 | ENST00000400454.6 | |
DSCAM | NM_001271534.3 | c.5388A>C | p.Arg1796= | synonymous_variant | 32/33 | ||
DSCAM | XM_017028281.2 | c.4680A>C | p.Arg1560= | synonymous_variant | 29/30 | ||
DSCAM | NR_073202.3 | n.5694A>C | non_coding_transcript_exon_variant | 32/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSCAM | ENST00000400454.6 | c.5388A>C | p.Arg1796= | synonymous_variant | 32/33 | 1 | NM_001389.5 | P1 | |
DSCAM | ENST00000404019.2 | c.4644A>C | p.Arg1548= | synonymous_variant | 28/29 | 1 | |||
DSCAM | ENST00000617870.4 | c.4893A>C | p.Arg1631= | synonymous_variant | 29/30 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00139 AC: 78AN: 56274Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.00107 AC: 205AN: 191766Hom.: 1 AF XY: 0.00134 AC XY: 141AN XY: 105048
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GnomAD4 exome AF: 0.000752 AC: 913AN: 1214706Hom.: 4 Cov.: 31 AF XY: 0.000943 AC XY: 553AN XY: 586716
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at