Genetic Variant GABPB1:c.*3053G>A (chr15-50275579-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016654.5(GABPB1):c.*3053G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,998 control chromosomes in the GnomAD database, including 36,501 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 0.68 ( 36501 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

GABPB1
NM_016654.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135

Publications

4 publications found

Variant links:

Genes affected

GABPB1 (HGNC:4074): (GA binding protein transcription factor subunit beta 1) This gene encodes the GA-binding protein transcription factor, beta subunit. This protein forms a tetrameric complex with the alpha subunit, and stimulates transcription of target genes. The encoded protein may be involved in activation of cytochrome oxidase expression and nuclear control of mitochondrial function. The crystal structure of a similar protein in mouse has been resolved as a ternary protein complex. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GABPB1 links:

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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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016654.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GABPB1	NM_016654.5	MANE Select	c.*3053G>A	3_prime_UTR	Exon 9 of 9	NP_057738.1	Q06547-2
GABPB1	NM_001320910.2		c.*3053G>A	3_prime_UTR	Exon 10 of 10	NP_001307839.1	Q06547-1
GABPB1	NM_005254.6		c.*3053G>A	3_prime_UTR	Exon 9 of 9	NP_005245.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.*3053G>A		3_prime_UTR	Exon 9 of 9	ENSP00000370259.3	Q06547-2

Frequencies

GnomAD3 genomes

AF:

0.684

AC:

103941

AN:

151880

Hom.:

36457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.819

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.707

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.650

Gnomad OTH

AF:

0.685

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.684

AC:

104042

AN:

151998

Hom.:

36501

Cov.:

AF XY:

0.675

AC XY:

50152

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.819

AC:

33984

AN:

41482

American (AMR)

AF:

0.707

AC:

10795

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.749

AC:

2596

AN:

3466

East Asian (EAS)

AF:

0.353

AC:

1818

AN:

5156

South Asian (SAS)

AF:

0.553

AC:

2663

AN:

4818

European-Finnish (FIN)

AF:

0.545

AC:

5752

AN:

10546

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.650

AC:

44175

AN:

67948

Other (OTH)

AF:

0.678

AC:

1433

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1587

3173

4760

6346

7933

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.658

Hom.:

17101

Bravo

AF:

0.707

Asia WGS

AF:

0.459

AC:

1598

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.1

(source)

DANN

Benign

0.33

PhyloP100

-0.14

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over