7-138628326-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001139456.2(SVOPL):c.901G>A(p.Ala301Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001139456.2 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 |
---|---|---|---|---|---|---|---|
SVOPL | NM_001139456.2 | c.901G>A | p.Ala301Thr | missense_variant | 11/16 | ENST00000674285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SVOPL | ENST00000674285.1 | c.901G>A | p.Ala301Thr | missense_variant | 11/16 | NM_001139456.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000390 AC: 98AN: 251238Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135794
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.000184 AC XY: 134AN XY: 727240
GnomAD4 genome AF: 0.000283 AC: 43AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.901G>A (p.A301T) alteration is located in exon 10 (coding exon 10) of the SVOPL gene. This alteration results from a G to A substitution at nucleotide position 901, causing the alanine (A) at amino acid position 301 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at