1-151098562-C-G

Position:

• chr1-151098562-C-G

Variant summary

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

The NM_144618.3(GABPB2):​c.622+560C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0893 in 149,360 control chromosomes in the GnomAD database, including 729 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 0.089 (729 hom., cov: 30)
• Consequence: GABPB2 NM_144618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

GABPB2 (HGNC:28441): (GA binding protein transcription factor subunit beta 2) Enables transcription cis-regulatory region binding activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABPB2	NM_144618.3	c.622+560C>G		intron_variant		ENST00000368918.8	NP_653219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABPB2	ENST00000368918.8	c.622+560C>G		intron_variant		1	NM_144618.3	ENSP00000357914.3
GABPB2	ENST00000467551.1	n.292+560C>G		intron_variant		1
GABPB2	ENST00000368916.1	c.622+560C>G		intron_variant		5		ENSP00000357912.1
GABPB2	ENST00000489549.5	n.660+560C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13330 AN: 149328 Hom.: 729 Cov.: 30

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0111

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0609

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0327

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0893 AC: 13343 AN: 149360 Hom.: 729 Cov.: 30 AF XY: 0.0868 AC XY: 6309 AN XY: 72672

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0609

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.0798

Gnomad4 NFE AF: 0.0756

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0313 Hom.: 16

Bravo AF: 0.0888

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
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: rs7537292; hg19: chr1-151071038;