chr15-50300346-C-T

Variant names:

• chr15-50300346-C-T
• rs2081628
• NM_016654.5:c.697+443G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016654.5(GABPB1):​c.697+443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 150,564 control chromosomes in the GnomAD database, including 18,072 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 (18072 hom., cov: 28)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.697+443G>A		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+443G>A		intron_variant	Intron 6 of 8	1	NM_016654.5	ENSP00000370259.3

Frequencies

GnomAD3 genomes AF: 0.471 AC: 70842 AN: 150450 Hom.: 18062 Cov.: 28

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.471 AC: 70891 AN: 150564 Hom.: 18072 Cov.: 28 AF XY: 0.461 AC XY: 33874 AN XY: 73450

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.504

Alfa AF: 0.504 Hom.: 2972

Bravo AF: 0.482

Asia WGS AF: 0.251 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs2081628; hg19: chr15-50592543;