1-223005136-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001377229.1(DISP1):c.3739G>T(p.Ala1247Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. A1247T) has been classified as Benign.
Frequency
Consequence
NM_001377229.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISP1 | NM_001377229.1 | c.3739G>T | p.Ala1247Ser | missense_variant | 9/9 | ENST00000675850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISP1 | ENST00000675850.1 | c.3739G>T | p.Ala1247Ser | missense_variant | 9/9 | NM_001377229.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000358 AC: 90AN: 251056Hom.: 0 AF XY: 0.000354 AC XY: 48AN XY: 135660
GnomAD4 exome AF: 0.000148 AC: 217AN: 1461872Hom.: 0 Cov.: 68 AF XY: 0.000151 AC XY: 110AN XY: 727232
GnomAD4 genome AF: 0.000204 AC: 31AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at