15-50369367-C-G

Variant names:

• chr15-50369367-C-G
• rs16963682
• ENST00000499624.4:n.13858C>G

Variant summary

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

The ENST00000499624.4(GABPB1-AS1):​n.13858C>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 ENST00000499624.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 0 publications found

Genes affected

GABPB1-AS1 (HGNC:44157): (GABPB1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499624.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1-AS1	ENST00000499624.4	TSL:1	n.13858C>G		non_coding_transcript_exon	Exon 2 of 2
	GABPB1-AS1	ENST00000738183.1		n.338C>G		non_coding_transcript_exon	Exon 3 of 5
	GABPB1-AS1	ENST00000738185.1		n.124C>G		non_coding_transcript_exon	Exon 2 of 3

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

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: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.130 AC: 4990 AN: 38442

American (AMR) AF: 0.0434 AC: 661 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.135 AC: 689 AN: 5116

South Asian (SAS) AF: 0.0873 AC: 421 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10590

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0685 AC: 4659 AN: 68016

Other (OTH) AF: 0.0635 AC: 133 AN: 2096

Alfa AF: 0.0244 Hom.: 16

Bravo AF: 0.0792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs16963682; hg19: chr15-50661564;