Genetic Variant GOLGA8IP:n.1671-5C>T (chr15-22608153-G-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000611635.4(GOLGA8IP):n.1671-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00594 in 1,503,580 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 21 hom., cov: 20)

Exomes 𝑓: 0.0059 ( 199 hom. )

Consequence

GOLGA8IP
ENST00000611635.4 splice_region, intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.821

Variant links:

Genes affected

GOLGA8IP (HGNC:26660): (golgin A8 family member I, pseudogene) 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]

GOLGA8IP links:

LOC101927846 (HGNC:):

LOC101927846 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 15-22608153-G-A is Benign according to our data. Variant chr15-22608153-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644959.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927846	XR_001751437.2 link	n.90-161G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8IP	ENST00000611635.4 link	n.1671-5C>T		splice_region_variant, intron_variant	Intron 15 of 17	6
ENSG00000291261	ENST00000647991.1 link	n.-27C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.00677

AC:

953

AN:

140854

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000674

Gnomad AMI

AF:

0.00225

Gnomad AMR

AF:

0.00193

Gnomad ASJ

AF:

0.00731

Gnomad EAS

AF:

0.000204

Gnomad SAS

AF:

0.00183

Gnomad FIN

AF:

0.0417

Gnomad MID

AF:

0.00325

Gnomad NFE

AF:

0.00678

Gnomad OTH

AF:

0.00421

GnomAD3 exomes

AF:

0.00437

AC:

321

AN:

73520

Hom.:

AF XY:

0.00452

AC XY:

169

AN XY:

37428

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00255

Gnomad ASJ exome

AF:

0.00730

Gnomad EAS exome

AF:

0.000242

Gnomad SAS exome

AF:

0.000940

Gnomad FIN exome

AF:

0.0423

Gnomad NFE exome

AF:

0.00568

Gnomad OTH exome

AF:

0.00295

GnomAD4 exome

AF:

0.00586

AC:

7979

AN:

1362640

Hom.:

199

Cov.:

AF XY:

0.00574

AC XY:

3911

AN XY:

681206

show subpopulations

Gnomad4 AFR exome

AF:

0.000635

Gnomad4 AMR exome

AF:

0.00245

Gnomad4 ASJ exome

AF:

0.00553

Gnomad4 EAS exome

AF:

0.0000257

Gnomad4 SAS exome

AF:

0.000768

Gnomad4 FIN exome

AF:

0.0417

Gnomad4 NFE exome

AF:

0.00549

Gnomad4 OTH exome

AF:

0.00570

GnomAD4 genome

AF:

0.00675

AC:

952

AN:

140940

Hom.:

Cov.:

AF XY:

0.00823

AC XY:

564

AN XY:

68490

show subpopulations

Gnomad4 AFR

AF:

0.000672

Gnomad4 AMR

AF:

0.00193

Gnomad4 ASJ

AF:

0.00731

Gnomad4 EAS

AF:

0.000204

Gnomad4 SAS

AF:

0.00161

Gnomad4 FIN

AF:

0.0417

Gnomad4 NFE

AF:

0.00678

Gnomad4 OTH

AF:

0.00418

Alfa

AF:

0.00673

Hom.:

Bravo

AF:

0.00330

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA8IP: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.25

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.33

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.33

Position offset: 30

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