NM_016654.5:c.109-994G>A

Variant names:

• chr15-50305127-C-T
• rs8031031
• NM_016654.5:c.109-994G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016654.5(GABPB1):​c.109-994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 152,096 control chromosomes in the GnomAD database, including 610 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 0.069 (610 hom., cov: 32)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.109-994G>A		intron_variant	Intron 2 of 8	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.109-994G>A		intron_variant	Intron 2 of 8	1	NM_016654.5	ENSP00000370259.3

Frequencies

GnomAD3 genomes AF: 0.0688 AC: 10459 AN: 151978 Hom.: 607 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0689 AC: 10479 AN: 152096 Hom.: 610 Cov.: 32 AF XY: 0.0714 AC XY: 5310 AN XY: 74344

African (AFR) AF: 0.140 AC: 5819 AN: 41464

American (AMR) AF: 0.0656 AC: 1002 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1031 AN: 5176

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4812

European-Finnish (FIN) AF: 0.0816 AC: 862 AN: 10568

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0186 AC: 1268 AN: 68012

Other (OTH) AF: 0.0581 AC: 123 AN: 2116

Alfa AF: 0.0571 Hom.: 159

Bravo AF: 0.0734

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.62
PhyloP100		0.86
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8031031; hg19: chr15-50597324;