rs7181866

chr15-50318595-A-G

Variant summary

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

The NM_016654.5(GABPB1):c.1-8797T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.066 in 152,218 control chromosomes in the GnomAD database, including 597 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 0.066 (597 hom., cov: 32)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

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 (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABPB1	NM_016654.5	c.1-8797T>C		intron_variant		ENST00000380877.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABPB1	ENST00000380877.8	c.1-8797T>C		intron_variant		1	NM_016654.5	P4

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10031 AN: 152102 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0660 AC: 10052 AN: 152218 Hom.: 597 Cov.: 32 AF XY: 0.0682 AC XY: 5076 AN XY: 74410

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0638

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.0149

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0399 Hom.: 67

Bravo AF: 0.0712

Asia WGS AF: 0.122 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.69

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: rs7181866; hg19: chr15-50610792;