rs1797311

Variant names:

• chr15-50312620-G-A
• rs1797311
• NM_016654.5:c.1-2822C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-50312620-G-A
• chr15-50312620-G-C
• chr15-50312620-G-T

Variant summary

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

The NM_016654.5(GABPB1):​c.1-2822C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,012 control chromosomes in the GnomAD database, including 9,430 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 0.33 (9430 hom., cov: 33)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.1-2822C>T		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.1-2822C>T		intron_variant	Intron 1 of 8	1	NM_016654.5	ENSP00000370259.3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50727 AN: 151892 Hom.: 9426 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.334 AC: 50751 AN: 152012 Hom.: 9430 Cov.: 33 AF XY: 0.342 AC XY: 25433 AN XY: 74278

African (AFR) AF: 0.175 AC: 7271 AN: 41494

American (AMR) AF: 0.316 AC: 4828 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 976 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2019 AN: 5178

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4816

European-Finnish (FIN) AF: 0.511 AC: 5367 AN: 10512

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27020 AN: 67954

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.260 Hom.: 763

Bravo AF: 0.307

Asia WGS AF: 0.429 AC: 1486 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.87
PhyloP100		0.20
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: rs1797311; hg19: chr15-50604817;