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GeneBe

15-50296361-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_016654.5(GABPB1):c.697+4428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,200 control chromosomes in the GnomAD database, including 6,489 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 0.26 ( 6489 hom., cov: 33)

Consequence

GABPB1
NM_016654.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.238
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GABPB1NM_016654.5 linkuse as main transcriptc.697+4428T>C intron_variant ENST00000380877.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GABPB1ENST00000380877.8 linkuse as main transcriptc.697+4428T>C intron_variant 1 NM_016654.5 P4Q06547-2

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39424
AN:
152082
Hom.:
6492
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0829
Gnomad AMI
AF:
0.512
Gnomad AMR
AF:
0.343
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.00654
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.244
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.362
Gnomad OTH
AF:
0.283
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.259
AC:
39418
AN:
152200
Hom.:
6489
Cov.:
33
AF XY:
0.254
AC XY:
18940
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0828
Gnomad4 AMR
AF:
0.343
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.00655
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.244
Gnomad4 NFE
AF:
0.362
Gnomad4 OTH
AF:
0.280
Alfa
AF:
0.342
Hom.:
12040
Bravo
AF:
0.262
Asia WGS
AF:
0.115
AC:
404
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
Cadd
Benign
9.8
Dann
Benign
0.90

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6493426; hg19: chr15-50588558; API