15-28702680-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001282468.3(GOLGA8M):āc.1434T>Cā(p.Leu478=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 29)
Exomes š: 0.0000062 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
GOLGA8M
NM_001282468.3 synonymous
NM_001282468.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
Genes affected
GOLGA8M (HGNC:44404): (golgin A8 family member M) Predicted to be involved in Golgi organization. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 15-28702680-A-G is Benign according to our data. Variant chr15-28702680-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3026287.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.076 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA8M | NM_001282468.3 | c.1434T>C | p.Leu478= | synonymous_variant | 16/19 | ENST00000563027.2 | |
LOC107984746 | XR_001751465.2 | n.90-48A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA8M | ENST00000563027.2 | c.1434T>C | p.Leu478= | synonymous_variant | 16/19 | 5 | NM_001282468.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151576Hom.: 0 Cov.: 29
GnomAD3 genomes
AF:
AC:
1
AN:
151576
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000288 AC: 7AN: 242960Hom.: 2 AF XY: 0.0000227 AC XY: 3AN XY: 132314
GnomAD3 exomes
AF:
AC:
7
AN:
242960
Hom.:
AF XY:
AC XY:
3
AN XY:
132314
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000619 AC: 9AN: 1454596Hom.: 2 Cov.: 37 AF XY: 0.00000691 AC XY: 5AN XY: 723844
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
9
AN:
1454596
Hom.:
Cov.:
37
AF XY:
AC XY:
5
AN XY:
723844
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000659 AC: 1AN: 151684Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74100
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
151684
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
74100
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | GOLGA8M: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at