rs17416784

Positions:

• chr15-50275958-T-C

Variant summary

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

The NM_016654.5(GABPB1):​c.*2674A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,208 control chromosomes in the GnomAD database, including 402 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 0.062 (402 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: GABPB1 NM_016654.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABPB1	NM_016654.5	c.*2674A>G		3_prime_UTR_variant	9/9	ENST00000380877.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABPB1	ENST00000380877.8	c.*2674A>G		3_prime_UTR_variant	9/9	1	NM_016654.5	P4

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9429 AN: 152090 Hom.: 403 Cov.: 33

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.0742

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0619 AC: 9429 AN: 152208 Hom.: 402 Cov.: 33 AF XY: 0.0620 AC XY: 4617 AN XY: 74422

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0783

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.0325

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0879

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0740 Hom.: 62

Bravo AF: 0.0570

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.53

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: rs17416784; hg19: chr15-50568155;