dbSNP rs200069148: GOLGA8Q:p.Pro557Pro (chr15-30562188-C-G) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

0 publications found

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:

ARHGAP11B-DT (HGNC:55586): (ARHGAP11B divergent transcript)

ARHGAP11B-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355476.2. 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
	GOLGA8Q	NM_001355476.2	MANE Select	c.1671C>G	p.Pro557Pro	synonymous	Exon 18 of 19	NP_001342405.1	H3BV12

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GOLGA8Q	ENST00000562783.2	TSL:5 MANE Select	c.1671C>G	p.Pro557Pro	synonymous	Exon 18 of 19	ENSP00000457904.1	H3BV12
ARHGAP11B-DT	ENST00000749391.1		n.538-21907G>C		intron	N/A
ARHGAP11B-DT	ENST00000749392.1		n.677-21907G>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.000667

AC:

AN:

77918

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.000477

AC:

AN:

27270

AF XY:

0.000288

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 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

African (AFR)

AF:

0.00

AC:

AN:

14434

American (AMR)

AF:

0.00

AC:

AN:

32376

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

393

AN:

17934

East Asian (EAS)

AF:

0.00

AC:

AN:

36084

South Asian (SAS)

AF:

0.00

AC:

AN:

63792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25458

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2850

European-Non Finnish (NFE)

AF:

0.0000891

AC:

AN:

763310

Other (OTH)

AF:

0.00195

AC:

AN:

41972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

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

African (AFR)

AF:

0.000152

AC:

AN:

13134

American (AMR)

AF:

0.00

AC:

AN:

9066

Ashkenazi Jewish (ASJ)

AF:

0.0209

AC:

AN:

2156

East Asian (EAS)

AF:

0.00

AC:

AN:

4352

South Asian (SAS)

AF:

0.00

AC:

AN:

2784

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5204

Middle Eastern (MID)

AF:

0.00

AC:

AN:

170

European-Non Finnish (NFE)

AF:

0.0000759

AC:

AN:

39512

Other (OTH)

AF:

0.00191

AC:

AN:

1046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.540

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.00

Hom.:

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

-0.94

CADD

Benign

1.5

(source)

DANN

Benign

0.43

PhyloP100

-0.58

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