rs2078139

Positions:

• chr15-50367637-C-T

Variant summary

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

The ENST00000499624.3(GABPB1-AS1):​n.11617C>T 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 0.212 in 151,462 control chromosomes in the GnomAD database, including 3,780 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 0.21 (3780 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: GABPB1-AS1 ENST00000499624.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABPB1-AS1	ENST00000499624.3	n.11617C>T		non_coding_transcript_exon_variant	2/2	1
GABPB1-AS1	ENST00000648591.1	n.449-2693C>T		intron_variant, non_coding_transcript_variant
GABPB1-AS1	ENST00000668321.1	n.87-2695C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32122 AN: 151348 Hom.: 3777 Cov.: 30

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.244

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: 0.212 AC: 32134 AN: 151462 Hom.: 3780 Cov.: 30 AF XY: 0.217 AC XY: 16021 AN XY: 73994

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.242

Alfa AF: 0.206 Hom.: 498

Bravo AF: 0.213

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2078139; hg19: chr15-50659834;