chr5-169593463-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017785.5(SPDL1):c.446G>A(p.Arg149His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000294 in 1,614,088 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 Uncertain significance (★).
Frequency
Consequence
NM_017785.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPDL1 | NM_017785.5 | c.446G>A | p.Arg149His | missense_variant | 4/12 | ENST00000265295.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDL1 | ENST00000265295.9 | c.446G>A | p.Arg149His | missense_variant | 4/12 | 1 | NM_017785.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251390Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135870
GnomAD4 exome AF: 0.000309 AC: 452AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.000308 AC XY: 224AN XY: 727222
GnomAD4 genome AF: 0.000151 AC: 23AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74434
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at