rs2609383
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001377229.1(DISP1):c.307G>A(p.Glu103Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,613,312 control chromosomes in the GnomAD database, including 21,708 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E103D) has been classified as Benign.
Frequency
Consequence
NM_001377229.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISP1 | NM_001377229.1 | c.307G>A | p.Glu103Lys | missense_variant | 3/9 | ENST00000675850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP1 | ENST00000675850.1 | c.307G>A | p.Glu103Lys | missense_variant | 3/9 | NM_001377229.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.162 AC: 24674AN: 151926Hom.: 2042 Cov.: 32
GnomAD3 exomes AF: 0.179 AC: 45021AN: 251192Hom.: 4534 AF XY: 0.182 AC XY: 24753AN XY: 135726
GnomAD4 exome AF: 0.156 AC: 228147AN: 1461268Hom.: 19654 Cov.: 33 AF XY: 0.159 AC XY: 115902AN XY: 726796
GnomAD4 genome ? AF: 0.163 AC: 24708AN: 152044Hom.: 2054 Cov.: 32 AF XY: 0.168 AC XY: 12479AN XY: 74322
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at