rs11634585

Variant names:

• chr15-50364252-G-A
• rs11634585
• ENST00000499624.3:n.8232G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-50364252-G-A
• chr15-50364252-G-T

Variant summary

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

The ENST00000499624.3(GABPB1-AS1):​n.8232G>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 ENST00000499624.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1-AS1	ENST00000499624.3	n.8232G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
GABPB1-AS1	ENST00000558593.1	n.449-3129G>A		intron_variant	Intron 1 of 1	5
GABPB1-AS1	ENST00000648591.1	n.449-6078G>A		intron_variant	Intron 2 of 2
GABPB1-AS1	ENST00000668321.1	n.87-6080G>A		intron_variant	Intron 1 of 1

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

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

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.647

Alfa AF: 0.658 Hom.: 21217

Bravo AF: 0.663

Asia WGS AF: 0.647 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.66
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

Publications

LitVar

Other links and lift over

dbSNP: rs11634585; hg19: chr15-50656449;