chr21-40042531-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001389.5(DSCAM):c.5526G>A(p.Thr1842=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,090 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 (★). 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>A | p.Thr1842= | synonymous_variant | 32/33 | ENST00000400454.6 | |
DSCAM | NM_001271534.3 | c.5526G>A | p.Thr1842= | synonymous_variant | 32/33 | ||
DSCAM | XM_017028281.2 | c.4818G>A | p.Thr1606= | synonymous_variant | 29/30 | ||
DSCAM | NR_073202.3 | n.5832G>A | non_coding_transcript_exon_variant | 32/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSCAM | ENST00000400454.6 | c.5526G>A | p.Thr1842= | synonymous_variant | 32/33 | 1 | NM_001389.5 | P1 | |
DSCAM | ENST00000404019.2 | c.4782G>A | p.Thr1594= | synonymous_variant | 28/29 | 1 | |||
DSCAM | ENST00000617870.4 | c.5031G>A | p.Thr1677= | synonymous_variant | 29/30 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000144 AC: 36AN: 249604Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135410
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727248
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at