chr15-50275579-C-T

Position:

• chr15-50275579-C-T

Variant summary

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

The NM_016654.5(GABPB1):​c.*3053G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,998 control chromosomes in the GnomAD database, including 36,501 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 0.68 (36501 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: GABPB1 NM_016654.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.*3053G>A		3_prime_UTR_variant	9/9	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.*3053G>A		3_prime_UTR_variant	9/9	1	NM_016654.5	ENSP00000370259	P4

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103941 AN: 151880 Hom.: 36457 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.685

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: 0.684 AC: 104042 AN: 151998 Hom.: 36501 Cov.: 31 AF XY: 0.675 AC XY: 50152 AN XY: 74296

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.678

Alfa AF: 0.655 Hom.: 15062

Bravo AF: 0.707

Asia WGS AF: 0.459 AC: 1598 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.33

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: rs2114447; hg19: chr15-50567776;