dbSNP rs1412892: GORAB:c.61+1092A>G (chr1-170533376-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152281.3(GORAB):c.61+1092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 292,008 control chromosomes in the GnomAD database, including 135,640 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.94 ( 67273 hom., cov: 31)

Exomes 𝑓: 0.99 ( 68367 hom. )

Consequence

GORAB
NM_152281.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670

Publications

3 publications found

Variant links:

Genes affected

GORAB (HGNC:25676): (golgin, RAB6 interacting) This gene encodes a member of the golgin family, a group of coiled-coil proteins localized to the Golgi. The encoded protein may function in the secretory pathway. The encoded protein, which also localizes to the cytoplasm, was identified by interactions with the N-terminal kinase-like protein, and thus it may function in mitosis. Mutations in this gene have been associated with geroderma osteodysplastica. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

GORAB links:

GORAB-AS1 (HGNC:54051): (GORAB antisense RNA 1)

GORAB-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GORAB	NM_152281.3 link	c.61+1092A>G		intron_variant	Intron 1 of 4	ENST00000367763.8	NP_689494.3	Q5T7V8-1B3KQ87

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GORAB	ENST00000367763.8 link	c.61+1092A>G		intron_variant	Intron 1 of 4	2	NM_152281.3	ENSP00000356737.4		Q5T7V8-1

Frequencies

GnomAD3 genomes

AF:

0.935

AC:

142282

AN:

152134

Hom.:

67237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.779

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.975

Gnomad ASJ

AF:

0.965

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.951

GnomAD4 exome

AF:

0.988

AC:

138115

AN:

139756

Hom.:

68367

AF XY:

0.990

AC XY:

76182

AN XY:

76914

show subpopulations

African (AFR)

AF:

0.781

AC:

4058

AN:

5196

American (AMR)

AF:

0.986

AC:

14153

AN:

14354

Ashkenazi Jewish (ASJ)

AF:

0.967

AC:

3263

AN:

3376

East Asian (EAS)

AF:

1.00

AC:

8021

AN:

8022

South Asian (SAS)

AF:

1.00

AC:

28773

AN:

28784

European-Finnish (FIN)

AF:

1.00

AC:

5552

AN:

5552

Middle Eastern (MID)

AF:

0.995

AC:

627

AN:

630

European-Non Finnish (NFE)

AF:

0.999

AC:

67331

AN:

67404

Other (OTH)

AF:

0.984

AC:

6337

AN:

6438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

142

213

284

355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.935

AC:

142371

AN:

152252

Hom.:

67273

Cov.:

AF XY:

0.937

AC XY:

69749

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.779

AC:

32325

AN:

41496

American (AMR)

AF:

0.975

AC:

14930

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.965

AC:

3347

AN:

3470

East Asian (EAS)

AF:

1.00

AC:

5172

AN:

5172

South Asian (SAS)

AF:

0.999

AC:

4825

AN:

4828

European-Finnish (FIN)

AF:

1.00

AC:

10620

AN:

10620

Middle Eastern (MID)

AF:

0.986

AC:

290

AN:

294

European-Non Finnish (NFE)

AF:

0.999

AC:

67940

AN:

68042

Other (OTH)

AF:

0.952

AC:

2012

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

404

809

1213

1618

2022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.959

Hom.:

8587

Bravo

AF:

0.927

Asia WGS

AF:

0.985

AC:

3427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.6

(source)

DANN

Benign

0.31

PhyloP100

-0.67

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over