rs370041442
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001389.5(DSCAM):c.5980G>T(p.Asp1994Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1994N) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DSCAM
NM_001389.5 missense
NM_001389.5 missense
Scores
5
9
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.34
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DSCAM | NM_001389.5 | c.5980G>T | p.Asp1994Tyr | missense_variant | Exon 33 of 33 | ENST00000400454.6 | NP_001380.2 | |
| DSCAM | NM_001271534.3 | c.5926G>T | p.Asp1976Tyr | missense_variant | Exon 33 of 33 | NP_001258463.1 | ||
| DSCAM | XM_017028281.2 | c.5272G>T | p.Asp1758Tyr | missense_variant | Exon 30 of 30 | XP_016883770.1 | ||
| DSCAM | NR_073202.3 | n.6286G>T | non_coding_transcript_exon_variant | Exon 33 of 33 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DSCAM | ENST00000400454.6 | c.5980G>T | p.Asp1994Tyr | missense_variant | Exon 33 of 33 | 1 | NM_001389.5 | ENSP00000383303.1 | ||
| DSCAM | ENST00000404019.2 | c.5182G>T | p.Asp1728Tyr | missense_variant | Exon 29 of 29 | 1 | ENSP00000385342.2 | |||
| DSCAM | ENST00000617870.4 | c.5485G>T | p.Asp1829Tyr | missense_variant | Exon 30 of 30 | 5 | ENSP00000478698.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1439076Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 712668
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1439076
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
712668
Gnomad4 AFR exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
M;.;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;.;N
REVEL
Uncertain
Sift
Uncertain
D;.;D
Sift4G
Uncertain
D;D;D
Polyphen
D;.;.
Vest4
MutPred
Gain of phosphorylation at D1994 (P = 0.0271);.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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