15-50337206-T-G

Variant names:

• chr15-50337206-T-G
• rs45508400
• NM_016654.5:c.-1+17779A>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.-1+17779A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 146,494 control chromosomes in the GnomAD database, including 7,511 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 0.29 (7511 hom., cov: 25)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.-1+17779A>C		intron_variant	Intron 1 of 8	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.-1+17779A>C		intron_variant	Intron 1 of 8	1	NM_016654.5	ENSP00000370259.3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 42079 AN: 146386 Hom.: 7511 Cov.: 25

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.00919

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.431

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.287 AC: 42085 AN: 146494 Hom.: 7511 Cov.: 25 AF XY: 0.283 AC XY: 20082 AN XY: 70928

African (AFR) AF: 0.105 AC: 4229 AN: 40436

American (AMR) AF: 0.373 AC: 5399 AN: 14484

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1074 AN: 3440

East Asian (EAS) AF: 0.00921 AC: 45 AN: 4884

South Asian (SAS) AF: 0.293 AC: 1335 AN: 4562

European-Finnish (FIN) AF: 0.282 AC: 2528 AN: 8980

Middle Eastern (MID) AF: 0.423 AC: 120 AN: 284

European-Non Finnish (NFE) AF: 0.395 AC: 26256 AN: 66536

Other (OTH) AF: 0.309 AC: 618 AN: 2002

Alfa AF: 0.304 Hom.: 3895

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		0.95
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: rs45508400; hg19: chr15-50629403;