chr19-38081781-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_015073.3(SIPA1L3):c.216C>T(p.Pro72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000366 in 1,610,896 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P72P) has been classified as Likely benign.
Frequency
Consequence
NM_015073.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIPA1L3 | NM_015073.3 | c.216C>T | p.Pro72= | synonymous_variant | 3/22 | ENST00000222345.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIPA1L3 | ENST00000222345.11 | c.216C>T | p.Pro72= | synonymous_variant | 3/22 | 1 | NM_015073.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000181 AC: 43AN: 238010Hom.: 1 AF XY: 0.000207 AC XY: 27AN XY: 130600
GnomAD4 exome AF: 0.000386 AC: 563AN: 1458648Hom.: 2 Cov.: 33 AF XY: 0.000411 AC XY: 298AN XY: 725570
GnomAD4 genome AF: 0.000177 AC: 27AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | SIPA1L3: BP4, BP7 - |
SIPA1L3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at