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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000716892.1(GOLGA8IP):n.405A>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
ENST00000716892.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.66

Publications

1 publications found

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:

GOLGA8IP (HGNC:):

GOLGA8IP links:

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

RN7SL495P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 2644956.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 13 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716892.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
GOLGA8IP	ENST00000611635.4	TSL:6	n.1406A>G	non_coding_transcript_exon	Exon 13 of 18
GOLGA8IP	ENST00000716892.1		n.405A>G	non_coding_transcript_exon	Exon 4 of 9
RN7SL495P	ENST00000616925.1	TSL:6	n.-123A>G	upstream_gene	N/A

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

GnomAD2 exomes

AF:

0.00129

AC:

289

AN:

224276

AF XY:

0.00152

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 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

African (AFR)

AF:

0.00305

AC:

102

AN:

33412

American (AMR)

AF:

0.000764

AC:

AN:

44498

Ashkenazi Jewish (ASJ)

AF:

0.0000766

AC:

AN:

26118

East Asian (EAS)

AF:

0.000933

AC:

AN:

39676

South Asian (SAS)

AF:

0.00592

AC:

508

AN:

85852

European-Finnish (FIN)

AF:

0.000160

AC:

AN:

43650

Middle Eastern (MID)

AF:

0.00110

AC:

AN:

4566

European-Non Finnish (NFE)

AF:

0.000351

AC:

390

AN:

1110990

Other (OTH)

AF:

0.00153

AC:

AN:

60124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

109

164

218

273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00130

AC:

198

AN:

152118

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

119

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.00238

AC:

AN:

41518

American (AMR)

AF:

0.000850

AC:

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3466

East Asian (EAS)

AF:

0.00233

AC:

AN:

5146

South Asian (SAS)

AF:

0.00769

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.000189

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000500

AC:

AN:

67960

Other (OTH)

AF:

0.000473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000304

Hom.:

Bravo

AF:

0.00111

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.2

(source)

DANN

Benign

0.23

PhyloP100

-1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over