15-50327518-G-A

Variant names:

• chr15-50327518-G-A
• rs11855823
• NM_016654.5:c.1-17720C>T

Variant summary

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

The NM_005254.6(GABPB1):​c.1-17720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,946 control chromosomes in the GnomAD database, including 19,501 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 0.49 (19501 hom., cov: 32)
• Consequence: GABPB1 NM_005254.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005254.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	NM_016654.5	MANE Select	c.1-17720C>T		intron	N/A	NP_057738.1
	GABPB1	NM_001320910.2		c.1-17720C>T		intron	N/A	NP_001307839.1
	GABPB1	NM_005254.6		c.1-17720C>T		intron	N/A	NP_005245.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.1-17720C>T		intron	N/A	ENSP00000370259.3
	GABPB1	ENST00000220429.12	TSL:1	c.1-17720C>T		intron	N/A	ENSP00000220429.8
	GABPB1	ENST00000429662.6	TSL:1	c.1-17720C>T		intron	N/A	ENSP00000395771.2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74713 AN: 151828 Hom.: 19482 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.492 AC: 74780 AN: 151946 Hom.: 19501 Cov.: 32 AF XY: 0.482 AC XY: 35776 AN XY: 74248

African (AFR) AF: 0.415 AC: 17200 AN: 41430

American (AMR) AF: 0.557 AC: 8505 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3468

East Asian (EAS) AF: 0.0567 AC: 294 AN: 5184

South Asian (SAS) AF: 0.459 AC: 2207 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3917 AN: 10522

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38425 AN: 67964

Other (OTH) AF: 0.518 AC: 1092 AN: 2108

Alfa AF: 0.516 Hom.: 3187

Bravo AF: 0.505

Asia WGS AF: 0.256 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.69
PhyloP100		0.22
PromoterAI		-0.0011	Neutral
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: rs11855823; hg19: chr15-50619715;