rs1797311

chr15-50312620-G-Achr15-50312620-G-Cchr15-50312620-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016654.5(GABPB1):c.1-2822C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,012 control chromosomes in the GnomAD database, including 9,430 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 0.33 (9430 hom., cov: 33)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABPB1	NM_016654.5	c.1-2822C>T		intron_variant		ENST00000380877.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABPB1	ENST00000380877.8	c.1-2822C>T		intron_variant		1	NM_016654.5	P4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50727 AN: 151892 Hom.: 9426 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.348

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.334 AC: 50751 AN: 152012 Hom.: 9430 Cov.: 33 AF XY: 0.342 AC XY: 25433 AN XY: 74278

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.352

Alfa AF: 0.260 Hom.: 763

Bravo AF: 0.307

Asia WGS AF: 0.429 AC: 1486 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.4
Dann	Benign	0.87

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

Other links and lift over

dbSNP: rs1797311; hg19: chr15-50604817;