chr15-50277152-T-G

Variant names:

• chr15-50277152-T-G
• rs3784296
• NM_016654.5:c.*1480A>C

Variant summary

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

The NM_016654.5(GABPB1):​c.*1480A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,938 control chromosomes in the GnomAD database, including 22,052 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 0.52 (22051 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: GABPB1 NM_016654.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	NM_016654.5	MANE Select	c.*1480A>C		3_prime_UTR	Exon 9 of 9	NP_057738.1
	GABPB1	NM_001320910.2		c.*1480A>C		3_prime_UTR	Exon 10 of 10	NP_001307839.1
	GABPB1	NM_005254.6		c.*1480A>C		3_prime_UTR	Exon 9 of 9	NP_005245.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.*1480A>C		3_prime_UTR	Exon 9 of 9	ENSP00000370259.3
	GABPB1	ENST00000220429.12	TSL:1	c.*1480A>C		downstream_gene	N/A	ENSP00000220429.8

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78636 AN: 151818 Hom.: 22037 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.518 AC: 78686 AN: 151936 Hom.: 22051 Cov.: 32 AF XY: 0.510 AC XY: 37869 AN XY: 74210

African (AFR) AF: 0.341 AC: 14128 AN: 41440

American (AMR) AF: 0.599 AC: 9137 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2527 AN: 3468

East Asian (EAS) AF: 0.150 AC: 776 AN: 5170

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4892 AN: 10506

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42888 AN: 67968

Other (OTH) AF: 0.559 AC: 1176 AN: 2104

Alfa AF: 0.595 Hom.: 110568

Bravo AF: 0.523

Asia WGS AF: 0.312 AC: 1090 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.73
PhyloP100		-0.036
Mutation Taster		=100/0	polymorphism

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: rs3784296; hg19: chr15-50569349;