Genetic Variant GOLGA8IP:n.1406A>G (chr15-22609500-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000611635.4(GOLGA8IP):n.1406A>G 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 0.000859 in 1,601,004 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 1 hom., cov: 31)

Exomes 𝑓: 0.00081 ( 13 hom. )

Consequence

GOLGA8IP
ENST00000611635.4 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.66

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:

RN7SL495P (HGNC:46511): (RNA, 7SL, cytoplasmic 495, pseudogene)

RN7SL495P links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 15-22609500-T-C is Benign according to our data. Variant chr15-22609500-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2644956.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927846	XR_001751437.2 link	n.186+1090T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA8IP	ENST00000611635.4 link	n.1406A>G		non_coding_transcript_exon_variant	Exon 13 of 18	6
RN7SL495P	ENST00000616925.1 link	n.-123A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.00126

AC:

191

AN:

152000

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00225

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000852

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00233

Gnomad SAS

AF:

0.00747

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000500

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00129

AC:

289

AN:

224276

Hom.:

AF XY:

0.00152

AC XY:

186

AN XY:

122092

show subpopulations

Gnomad AFR exome

AF:

0.00235

Gnomad AMR exome

AF:

0.000644

Gnomad ASJ exome

AF:

0.000208

Gnomad EAS exome

AF:

0.00135

Gnomad SAS exome

AF:

0.00592

Gnomad FIN exome

AF:

0.000144

Gnomad NFE exome

AF:

0.000385

Gnomad OTH exome

AF:

0.000351

GnomAD4 exome

AF:

0.000812

AC:

1177

AN:

1448886

Hom.:

Cov.:

AF XY:

0.000961

AC XY:

693

AN XY:

720868

show subpopulations

Gnomad4 AFR exome

AF:

0.00305

Gnomad4 AMR exome

AF:

0.000764

Gnomad4 ASJ exome

AF:

0.0000766

Gnomad4 EAS exome

AF:

0.000933

Gnomad4 SAS exome

AF:

0.00592

Gnomad4 FIN exome

AF:

0.000160

Gnomad4 NFE exome

AF:

0.000351

Gnomad4 OTH exome

AF:

0.00153

GnomAD4 genome

AF:

0.00130

AC:

198

AN:

152118

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

119

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.00238

Gnomad4 AMR

AF:

0.000850

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00233

Gnomad4 SAS

AF:

0.00769

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000500

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000304

Hom.:

Bravo

AF:

0.00111

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: PP2, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.2

DANN

Benign

0.23

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