chr15-50369367-C-G

Position:

• chr15-50369367-C-G

Variant summary

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

The ENST00000499624.3(GABPB1-AS1):​n.13347C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0854 in 148,990 control chromosomes in the GnomAD database, including 566 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 0.085 (566 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GABPB1-AS1 ENST00000499624.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

GABPB1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50369367C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABPB1-AS1	ENST00000499624.3	n.13347C>G		non_coding_transcript_exon_variant	2/2	1
GABPB1-AS1	ENST00000648591.1	n.449-963C>G		intron_variant
GABPB1-AS1	ENST00000668321.1	n.87-965C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12706 AN: 148868 Hom.: 564 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0593

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0854 AC: 12727 AN: 148990 Hom.: 566 Cov.: 33 AF XY: 0.0869 AC XY: 6335 AN XY: 72908

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0873

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0244 Hom.: 16

Bravo AF: 0.0792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16963682; hg19: chr15-50661564;