Genetic Variant GOLGA8IP:n.1182T>C (chr15-22611325-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000340249.4(GOLGA8IP):n.1182T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,601,726 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., cov: 26)

Exomes 𝑓: 0.0058 ( 46 hom. )

Consequence

GOLGA8IP
ENST00000340249.4 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.432

Variant links:

Genes affected

GOLGA8IP (HGNC:):

GOLGA8IP links:

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 15-22611325-A-G is Benign according to our data. Variant chr15-22611325-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2644955.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA8IP	NR_024074.2 link	n.1182T>C		non_coding_transcript_exon_variant	Exon 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8IP	ENST00000340249.4 link	n.1182T>C		non_coding_transcript_exon_variant	Exon 11 of 12	2
GOLGA8IP	ENST00000611635.4 link	n.1084T>C		non_coding_transcript_exon_variant	Exon 11 of 18	6

Frequencies

GnomAD3 genomes

AF:

0.00421

AC:

632

AN:

150180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00124

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.00265

Gnomad ASJ

AF:

0.00433

Gnomad EAS

AF:

0.000778

Gnomad SAS

AF:

0.00234

Gnomad FIN

AF:

0.000381

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00709

Gnomad OTH

AF:

0.000971

GnomAD3 exomes

AF:

0.00346

AC:

822

AN:

237312

Hom.:

AF XY:

0.00354

AC XY:

460

AN XY:

130096

show subpopulations

Gnomad AFR exome

AF:

0.000841

Gnomad AMR exome

AF:

0.00177

Gnomad ASJ exome

AF:

0.00455

Gnomad EAS exome

AF:

0.000277

Gnomad SAS exome

AF:

0.00151

Gnomad FIN exome

AF:

0.000411

Gnomad NFE exome

AF:

0.00571

Gnomad OTH exome

AF:

0.00354

GnomAD4 exome

AF:

0.00577

AC:

8369

AN:

1451434

Hom.:

Cov.:

AF XY:

0.00568

AC XY:

4100

AN XY:

722374

show subpopulations

Gnomad4 AFR exome

AF:

0.00144

Gnomad4 AMR exome

AF:

0.00197

Gnomad4 ASJ exome

AF:

0.00455

Gnomad4 EAS exome

AF:

0.000453

Gnomad4 SAS exome

AF:

0.00151

Gnomad4 FIN exome

AF:

0.000356

Gnomad4 NFE exome

AF:

0.00692

Gnomad4 OTH exome

AF:

0.00414

GnomAD4 genome

AF:

0.00423

AC:

636

AN:

150292

Hom.:

Cov.:

AF XY:

0.00379

AC XY:

278

AN XY:

73382

show subpopulations

Gnomad4 AFR

AF:

0.00136

Gnomad4 AMR

AF:

0.00258

Gnomad4 ASJ

AF:

0.00433

Gnomad4 EAS

AF:

0.000781

Gnomad4 SAS

AF:

0.00235

Gnomad4 FIN

AF:

0.000381

Gnomad4 NFE

AF:

0.00709

Gnomad4 OTH

AF:

0.000961

Alfa

AF:

0.00483

Hom.:

Bravo

AF:

0.00422

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, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.8

DANN

Benign

0.35

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