chr21-40042531-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001389.5(DSCAM):āc.5526G>Cā(p.Thr1842=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,614,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. T1842T) has been classified as Likely benign.
Frequency
Consequence
NM_001389.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSCAM | NM_001389.5 | c.5526G>C | p.Thr1842= | synonymous_variant | 32/33 | ENST00000400454.6 | |
DSCAM | NM_001271534.3 | c.5526G>C | p.Thr1842= | synonymous_variant | 32/33 | ||
DSCAM | XM_017028281.2 | c.4818G>C | p.Thr1606= | synonymous_variant | 29/30 | ||
DSCAM | NR_073202.3 | n.5832G>C | non_coding_transcript_exon_variant | 32/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSCAM | ENST00000400454.6 | c.5526G>C | p.Thr1842= | synonymous_variant | 32/33 | 1 | NM_001389.5 | P1 | |
DSCAM | ENST00000404019.2 | c.4782G>C | p.Thr1594= | synonymous_variant | 28/29 | 1 | |||
DSCAM | ENST00000617870.4 | c.5031G>C | p.Thr1677= | synonymous_variant | 29/30 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000140 AC: 35AN: 249604Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135410
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727248
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at