17-4487868-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_182538.5(SPNS3):c.1513G>A(p.Ala505Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,046 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 Likely benign (★).
Frequency
Consequence
NM_182538.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPNS3 | ENST00000355530.7 | c.1513G>A | p.Ala505Thr | missense_variant | Exon 12 of 12 | 2 | NM_182538.5 | ENSP00000347721.2 | ||
SPNS3 | ENST00000575194.5 | n.*767G>A | non_coding_transcript_exon_variant | Exon 11 of 11 | 1 | ENSP00000460781.1 | ||||
SPNS3 | ENST00000575194.5 | n.*767G>A | 3_prime_UTR_variant | Exon 11 of 11 | 1 | ENSP00000460781.1 | ||||
SPNS3 | ENST00000575796.1 | n.*6G>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251228Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135826
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461656Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727134
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152390Hom.: 0 Cov.: 34 AF XY: 0.0000268 AC XY: 2AN XY: 74526
ClinVar
Submissions by phenotype
not specified Benign:1
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