15-50364252-G-A

Variant names:

• chr15-50364252-G-A
• rs11634585
• ENST00000499624.4:n.8743G>A

Variant summary

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

The ENST00000499624.4(GABPB1-AS1):​n.8743G>A 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 0.649 in 151,906 control chromosomes in the GnomAD database, including 32,314 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 0.65 (32314 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: GABPB1-AS1 ENST00000499624.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.733 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABPB1-AS1	ENST00000499624.4	TSL:1	n.8743G>A		non_coding_transcript_exon	Exon 2 of 2
	GABPB1-AS1	ENST00000558593.1	TSL:5	n.449-3129G>A		intron	N/A
	GABPB1-AS1	ENST00000648591.1		n.449-6078G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98555 AN: 151786 Hom.: 32277 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.646

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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.649 AC: 98656 AN: 151906 Hom.: 32314 Cov.: 31 AF XY: 0.645 AC XY: 47900 AN XY: 74260

African (AFR) AF: 0.669 AC: 27694 AN: 41376

American (AMR) AF: 0.691 AC: 10556 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2498 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2570 AN: 5162

South Asian (SAS) AF: 0.754 AC: 3632 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5607 AN: 10544

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43941 AN: 67960

Other (OTH) AF: 0.647 AC: 1359 AN: 2102

Alfa AF: 0.656 Hom.: 29198

Bravo AF: 0.663

Asia WGS AF: 0.647 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.66
PhyloP100		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs11634585; hg19: chr15-50656449;