NM_016654.5:c.1000-1620T>C

Variant names:

• chr15-50280404-A-G
• rs12910368
• NM_016654.5:c.1000-1620T>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.1000-1620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,176 control chromosomes in the GnomAD database, including 1,509 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 0.13 (1509 hom., cov: 31)
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABPB1	NM_016654.5	c.1000-1620T>C		intron_variant	Intron 8 of 8	ENST00000380877.8	NP_057738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1	ENST00000380877.8	c.1000-1620T>C		intron_variant	Intron 8 of 8	1	NM_016654.5	ENSP00000370259.3
GABPB1	ENST00000220429.12	c.1036-1620T>C		intron_variant	Intron 8 of 8	1		ENSP00000220429.8
GABPB1	ENST00000543881.5	c.808-1620T>C		intron_variant	Intron 7 of 7	2		ENSP00000442500.1
GABPB1	ENST00000561010.5	c.*15-1620T>C		intron_variant	Intron 5 of 5	3		ENSP00000453806.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19396 AN: 152058 Hom.: 1507 Cov.: 31

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.128 AC: 19406 AN: 152176 Hom.: 1509 Cov.: 31 AF XY: 0.126 AC XY: 9388 AN XY: 74392

African (AFR) AF: 0.0683 AC: 2838 AN: 41534

American (AMR) AF: 0.157 AC: 2391 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3470

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5184

South Asian (SAS) AF: 0.163 AC: 786 AN: 4812

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10383 AN: 67984

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.130 Hom.: 973

Bravo AF: 0.129

Asia WGS AF: 0.0980 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.32
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: rs12910368; hg19: chr15-50572601;