Variant 15-30562188-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001355476.2(GOLGA8Q):c.1671C>G(p.Pro557Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000544 in 998,210 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00067 ( 14 hom., cov: 10)

Exomes 𝑓: 0.00054 ( 192 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA8Q
NM_001355476.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.582

Variant links:

Genes affected

GOLGA8Q (HGNC:44408): (golgin A8 family member Q) 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]

GOLGA8Q links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 15-30562188-C-G is Benign according to our data. Variant chr15-30562188-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2645107.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.582 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 192 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA8Q	NM_001355476.2 linkuse as main transcript	c.1671C>G	p.Pro557Pro	synonymous_variant	18/19	ENST00000562783.2	NP_001342405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLGA8Q	ENST00000562783.2 linkuse as main transcript	c.1671C>G	p.Pro557Pro	synonymous_variant	18/19	5	NM_001355476.2	ENSP00000457904.1		H3BV12

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

77918

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.0209

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000759

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.000477

AC:

AN:

27270

Hom.:

AF XY:

0.000288

AC XY:

AN XY:

13884

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.0202

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00110

GnomAD4 exome

AF:

0.000544

AC:

543

AN:

998210

Hom.:

192

Cov.:

AF XY:

0.000558

AC XY:

276

AN XY:

494818

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0219

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000891

Gnomad4 OTH exome

AF:

0.00195

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000667

AC:

AN:

77918

Hom.:

Cov.:

AF XY:

0.000611

AC XY:

AN XY:

37616

show subpopulations

Gnomad4 AFR

AF:

0.000152

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.0209

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000759

Gnomad4 OTH

AF:

0.00191

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, 2023

GOLGA8Q: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.5

DANN

Benign

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over