5-169588463-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017785.5(SPDL1):c.47C>T(p.Ala16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000955 in 1,613,372 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_017785.5 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 |
---|---|---|---|---|---|---|---|
SPDL1 | NM_017785.5 | c.47C>T | p.Ala16Val | missense_variant | 2/12 | ENST00000265295.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDL1 | ENST00000265295.9 | c.47C>T | p.Ala16Val | missense_variant | 2/12 | 1 | NM_017785.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250556Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135426
GnomAD4 exome AF: 0.0000986 AC: 144AN: 1461154Hom.: 1 Cov.: 30 AF XY: 0.000128 AC XY: 93AN XY: 726846
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at