Genetic Variant NM_001002296.2:c.*1199T>G (chr8-41510767-T-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_001002296.2(GOLGA7):c.*1199T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,784 control chromosomes in the GnomAD database, including 65,637 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 0.93 ( 65386 hom., cov: 32)

Exomes 𝑓: 0.95 ( 251 hom. )

Consequence

GOLGA7
NM_001002296.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.53

Publications

14 publications found

Variant links:

Genes affected

GOLGA7 (HGNC:24876): (golgin A7) Involved in Golgi to plasma membrane protein transport; peptidyl-L-cysteine S-palmitoylation; and protein stabilization. Acts upstream of or within Golgi to plasma membrane transport. Located in Golgi membrane and Golgi stack. Is intrinsic component of Golgi membrane. Part of palmitoyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA7 links:

GPAT4-AS1 (HGNC:55539): (GPAT4 and GINS4 antisense RNA 1)

GPAT4-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=-0.6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA7	NM_001002296.2 link	c.*1199T>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000357743.9	NP_001002296.1	Q7Z5G4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GOLGA7	ENST00000357743.9 link	c.*1199T>G	3_prime_UTR_variant	Exon 5 of 5	1	NM_001002296.2	ENSP00000350378.4	Q7Z5G4-1
GOLGA7	ENST00000405786.3 link	c.*1213T>G	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000386030.2	Q7Z5G4-3
GOLGA7	ENST00000694877.1 link	c.*1213T>G	3_prime_UTR_variant	Exon 6 of 6			ENSP00000511562.1	Q7Z5G4-3
GOLGA7	ENST00000694878.1 link	c.*1213T>G	3_prime_UTR_variant	Exon 5 of 5			ENSP00000511563.1	Q7Z5G4-3
GOLGA7	ENST00000694883.1 link	c.*1213T>G	3_prime_UTR_variant	Exon 6 of 6			ENSP00000511567.1	Q7Z5G4-3
GOLGA7	ENST00000694915.1 link	c.*1213T>G	3_prime_UTR_variant	Exon 6 of 6			ENSP00000511590.1	A0A8Q3WLN5

Frequencies

GnomAD3 genomes

AF:

0.926

AC:

140795

AN:

152112

Hom.:

65343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.887

Gnomad AMI

AF:

0.975

Gnomad AMR

AF:

0.926

Gnomad ASJ

AF:

0.988

Gnomad EAS

AF:

0.783

Gnomad SAS

AF:

0.924

Gnomad FIN

AF:

0.940

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.954

Gnomad OTH

AF:

0.928

GnomAD4 exome

AF:

0.953

AC:

528

AN:

554

Hom.:

251

Cov.:

AF XY:

0.949

AC XY:

336

AN XY:

354

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.875

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.946

AC:

405

AN:

428

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.979

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

AF:

0.926

AC:

140896

AN:

152230

Hom.:

65386

Cov.:

AF XY:

0.923

AC XY:

68713

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.887

AC:

36816

AN:

41512

American (AMR)

AF:

0.926

AC:

14158

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.988

AC:

3428

AN:

3470

East Asian (EAS)

AF:

0.783

AC:

4054

AN:

5180

South Asian (SAS)

AF:

0.924

AC:

4464

AN:

4830

European-Finnish (FIN)

AF:

0.940

AC:

9970

AN:

10612

Middle Eastern (MID)

AF:

0.966

AC:

284

AN:

294

European-Non Finnish (NFE)

AF:

0.954

AC:

64876

AN:

68014

Other (OTH)

AF:

0.927

AC:

1957

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

516

1032

1549

2065

2581

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:

0.940

Hom.:

32519

Bravo

AF:

0.921

Asia WGS

AF:

0.868

AC:

3020

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

2.5

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

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