5-169588429-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017785.5(SPDL1):āc.13A>Gā(p.Ile5Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,610,006 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_017785.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPDL1 | NM_017785.5 | c.13A>G | p.Ile5Val | missense_variant | 2/12 | ENST00000265295.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDL1 | ENST00000265295.9 | c.13A>G | p.Ile5Val | missense_variant | 2/12 | 1 | NM_017785.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000932 AC: 230AN: 246684Hom.: 0 AF XY: 0.00103 AC XY: 137AN XY: 133410
GnomAD4 exome AF: 0.00107 AC: 1559AN: 1457634Hom.: 3 Cov.: 30 AF XY: 0.00109 AC XY: 787AN XY: 725024
GnomAD4 genome AF: 0.000794 AC: 121AN: 152372Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74518
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at