chr15-50346480-A-C

Variant names:

• chr15-50346480-A-C
• rs16963644
• NM_016654.5:c.-1+8505T>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.-1+8505T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 152,310 control chromosomes in the GnomAD database, including 110 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 0.021 (110 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GABPB1 NM_016654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.78
• Publications: 4 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016654.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	NM_016654.5	MANE Select	c.-1+8505T>G		intron	N/A	NP_057738.1	Q06547-2
	GABPB1	NM_001320910.2		c.-24-85T>G		intron	N/A	NP_001307839.1	Q06547-1
	GABPB1	NM_005254.6		c.-1+8505T>G		intron	N/A	NP_005245.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1	ENST00000380877.8	TSL:1 MANE Select	c.-1+8505T>G		intron	N/A	ENSP00000370259.3	Q06547-2
	GABPB1	ENST00000220429.12	TSL:1	c.-1+8505T>G		intron	N/A	ENSP00000220429.8	Q06547-1
	GABPB1	ENST00000429662.6	TSL:1	c.-1+8505T>G		intron	N/A	ENSP00000395771.2	Q06547-3

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3176 AN: 152192 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00514

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0263

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0208 AC: 3164 AN: 152310 Hom.: 110 Cov.: 32 AF XY: 0.0234 AC XY: 1743 AN XY: 74492

African (AFR) AF: 0.00512 AC: 213 AN: 41574

American (AMR) AF: 0.0380 AC: 582 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3468

East Asian (EAS) AF: 0.102 AC: 528 AN: 5180

South Asian (SAS) AF: 0.148 AC: 713 AN: 4826

European-Finnish (FIN) AF: 0.00960 AC: 102 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0126 AC: 860 AN: 68024

Other (OTH) AF: 0.0270 AC: 57 AN: 2112

Alfa AF: 0.0156 Hom.: 20

Bravo AF: 0.0202

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		2.8
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: rs16963644; hg19: chr15-50638677;