rs11634585

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABPB1-AS1	ENST00000499624.3	n.8232G>A		non_coding_transcript_exon_variant	2/2	1
GABPB1-AS1	ENST00000558593.1	n.449-3129G>A		intron_variant, non_coding_transcript_variant		5
GABPB1-AS1	ENST00000648591.1	n.449-6078G>A		intron_variant, non_coding_transcript_variant
GABPB1-AS1	ENST00000668321.1	n.87-6080G>A		intron_variant, non_coding_transcript_variant

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;