rs12594956

Variant names:

• chr15-50329637-C-A
• rs12594956
• NM_016654.5:c.1-19839G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-50329637-C-A
• chr15-50329637-C-G

Variant summary

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

The NM_016654.5(GABPB1):​c.1-19839G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,896 control chromosomes in the GnomAD database, including 30,823 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 0.63 (30823 hom., cov: 31)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 27 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016654.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	NM_016654.5	MANE Select	c.1-19839G>T		intron	N/A	NP_057738.1	Q06547-2
	GABPB1	NM_001320910.2		c.-1+16735G>T		intron	N/A	NP_001307839.1	Q06547-1
	GABPB1	NM_005254.6		c.1-19839G>T		intron	N/A	NP_005245.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.1-19839G>T		intron	N/A	ENSP00000370259.3	Q06547-2
	GABPB1	ENST00000220429.12	TSL:1	c.1-19839G>T		intron	N/A	ENSP00000220429.8	Q06547-1
	GABPB1	ENST00000429662.6	TSL:1	c.1-19839G>T		intron	N/A	ENSP00000395771.2	Q06547-3

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95061 AN: 151778 Hom.: 30783 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.626 AC: 95155 AN: 151896 Hom.: 30823 Cov.: 31 AF XY: 0.617 AC XY: 45783 AN XY: 74216

African (AFR) AF: 0.769 AC: 31875 AN: 41472

American (AMR) AF: 0.655 AC: 10000 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2432 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5158

South Asian (SAS) AF: 0.527 AC: 2542 AN: 4820

European-Finnish (FIN) AF: 0.454 AC: 4765 AN: 10488

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39735 AN: 67920

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.615 Hom.: 4808

Bravo AF: 0.652

Asia WGS AF: 0.430 AC: 1490 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.19
PhyloP100		-0.18
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: rs12594956; hg19: chr15-50621834;