1-57010703-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365792.1(DAB1):c.1660G>T(p.Gly554Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000798 in 1,571,932 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G554S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365792.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAB1 | NM_001365792.1 | c.1660G>T | p.Gly554Cys | missense_variant | 14/15 | ENST00000371236.7 | |
LOC112267900 | XR_007066117.1 | n.11371C>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAB1 | ENST00000371236.7 | c.1660G>T | p.Gly554Cys | missense_variant | 14/15 | 5 | NM_001365792.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00429 AC: 653AN: 152134Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00112 AC: 263AN: 235822Hom.: 3 AF XY: 0.000838 AC XY: 107AN XY: 127700
GnomAD4 exome AF: 0.000423 AC: 600AN: 1419680Hom.: 3 Cov.: 29 AF XY: 0.000386 AC XY: 271AN XY: 702820
GnomAD4 genome ? AF: 0.00430 AC: 655AN: 152252Hom.: 6 Cov.: 33 AF XY: 0.00416 AC XY: 310AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at