15-50298597-T-C

Variant names:

• chr15-50298597-T-C
• rs17508371
• NM_016654.5:c.697+2192A>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.697+2192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,976 control chromosomes in the GnomAD database, including 18,420 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 0.47 (18420 hom., cov: 32)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.697+2192A>G		intron_variant	Intron 6 of 8	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.697+2192A>G		intron_variant	Intron 6 of 8	1	NM_016654.5	ENSP00000370259.3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71937 AN: 151858 Hom.: 18408 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.474 AC: 71991 AN: 151976 Hom.: 18420 Cov.: 32 AF XY: 0.464 AC XY: 34488 AN XY: 74282

African (AFR) AF: 0.349 AC: 14477 AN: 41454

American (AMR) AF: 0.553 AC: 8436 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3468

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5182

South Asian (SAS) AF: 0.460 AC: 2214 AN: 4818

European-Finnish (FIN) AF: 0.374 AC: 3946 AN: 10542

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38415 AN: 67946

Other (OTH) AF: 0.507 AC: 1069 AN: 2108

Alfa AF: 0.505 Hom.: 3448

Bravo AF: 0.485

Asia WGS AF: 0.255 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		-2.1
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: rs17508371; hg19: chr15-50590794;