NM_016654.5:c.*793T>C

Variant names:

• chr15-50277839-A-G
• rs12923
• NM_016654.5:c.*793T>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.*793T>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 0.164 in 152,584 control chromosomes in the GnomAD database, including 2,210 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 0.16 (2208 hom., cov: 32)
  • Exomes 𝑓: 0.11 (2 hom.)
• Consequence: GABPB1 NM_016654.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 6 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=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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.*793T>C		3_prime_UTR	Exon 9 of 9	NP_057738.1	Q06547-2
	GABPB1	NM_001320910.2		c.*793T>C		3_prime_UTR	Exon 10 of 10	NP_001307839.1	Q06547-1
	GABPB1	NM_005254.6		c.*793T>C		3_prime_UTR	Exon 9 of 9	NP_005245.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.*793T>C		3_prime_UTR	Exon 9 of 9	ENSP00000370259.3	Q06547-2
	GABPB1	ENST00000220429.12	TSL:1	c.*793T>C		3_prime_UTR	Exon 9 of 9	ENSP00000220429.8	Q06547-1
	GABPB1	ENST00000901079.1		c.*793T>C		3_prime_UTR	Exon 10 of 10	ENSP00000571138.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24881 AN: 152048 Hom.: 2206 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.110 AC: 46 AN: 420 Hom.: 2 Cov.: 0 AF XY: 0.113 AC XY: 29 AN XY: 256

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) AF: 0.111 AC: 46 AN: 414

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.164 AC: 24913 AN: 152164 Hom.: 2208 Cov.: 32 AF XY: 0.161 AC XY: 11986 AN XY: 74408

African (AFR) AF: 0.196 AC: 8138 AN: 41522

American (AMR) AF: 0.165 AC: 2521 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3468

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5188

South Asian (SAS) AF: 0.164 AC: 792 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10404 AN: 67972

Other (OTH) AF: 0.178 AC: 377 AN: 2114

Alfa AF: 0.163 Hom.: 1292

Bravo AF: 0.170

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		0.48
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: rs12923; hg19: chr15-50570036;