rs12906304

Variant names:

• chr15-50280201-C-T
• rs12906304
• NM_016654.5:c.1000-1417G>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.1000-1417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,042 control chromosomes in the GnomAD database, including 2,394 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 0.17 (2394 hom., cov: 31)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.1000-1417G>A		intron_variant	Intron 8 of 8	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.1000-1417G>A		intron_variant	Intron 8 of 8	1	NM_016654.5	ENSP00000370259.3
GABPB1	ENST00000220429.12	c.1036-1417G>A		intron_variant	Intron 8 of 8	1		ENSP00000220429.8
GABPB1	ENST00000543881.5	c.808-1417G>A		intron_variant	Intron 7 of 7	2		ENSP00000442500.1
GABPB1	ENST00000561010.5	c.*15-1417G>A		intron_variant	Intron 5 of 5	3		ENSP00000453806.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25827 AN: 151924 Hom.: 2387 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.170 AC: 25873 AN: 152042 Hom.: 2394 Cov.: 31 AF XY: 0.168 AC XY: 12450 AN XY: 74322

African (AFR) AF: 0.219 AC: 9071 AN: 41466

American (AMR) AF: 0.167 AC: 2544 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3470

East Asian (EAS) AF: 0.0488 AC: 252 AN: 5160

South Asian (SAS) AF: 0.164 AC: 789 AN: 4806

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10578

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10413 AN: 67986

Other (OTH) AF: 0.178 AC: 375 AN: 2106

Alfa AF: 0.170 Hom.: 390

Bravo AF: 0.177

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.47
PhyloP100		-0.0020
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: rs12906304; hg19: chr15-50572398;