21-40042448-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001389.5(DSCAM):c.5609G>A(p.Arg1870Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,202 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001389.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DSCAM | NM_001389.5 | c.5609G>A | p.Arg1870Lys | missense_variant | Exon 32 of 33 | ENST00000400454.6 | NP_001380.2 | |
DSCAM | NM_001271534.3 | c.5609G>A | p.Arg1870Lys | missense_variant | Exon 32 of 33 | NP_001258463.1 | ||
DSCAM | XM_017028281.2 | c.4901G>A | p.Arg1634Lys | missense_variant | Exon 29 of 30 | XP_016883770.1 | ||
DSCAM | NR_073202.3 | n.5915G>A | non_coding_transcript_exon_variant | Exon 32 of 33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DSCAM | ENST00000400454.6 | c.5609G>A | p.Arg1870Lys | missense_variant | Exon 32 of 33 | 1 | NM_001389.5 | ENSP00000383303.1 | ||
DSCAM | ENST00000404019.2 | c.4865G>A | p.Arg1622Lys | missense_variant | Exon 28 of 29 | 1 | ENSP00000385342.2 | |||
DSCAM | ENST00000617870.4 | c.5114G>A | p.Arg1705Lys | missense_variant | Exon 29 of 30 | 5 | ENSP00000478698.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.5609G>A (p.R1870K) alteration is located in exon 32 (coding exon 32) of the DSCAM gene. This alteration results from a G to A substitution at nucleotide position 5609, causing the arginine (R) at amino acid position 1870 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at