rs11855823

Positions:

• chr15-50327518-G-A

Variant summary

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

The NM_016654.5(GABPB1):​c.1-17720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,946 control chromosomes in the GnomAD database, including 19,501 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 0.49 (19501 hom., cov: 32)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.1-17720C>T		intron_variant		ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.1-17720C>T		intron_variant		1	NM_016654.5	ENSP00000370259	P4

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74713 AN: 151828 Hom.: 19482 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.492 AC: 74780 AN: 151946 Hom.: 19501 Cov.: 32 AF XY: 0.482 AC XY: 35776 AN XY: 74248

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.0567

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.518

Alfa AF: 0.519 Hom.: 3107

Bravo AF: 0.505

Asia WGS AF: 0.256 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
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: rs11855823; hg19: chr15-50619715;