rs17431095

chr15-50369252-A-G

Variant summary

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

The ENST00000499624.3(GABPB1-AS1):n.13232A>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 0.274 in 152,184 control chromosomes in the GnomAD database, including 7,156 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 0.27 (7155 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: GABPB1-AS1 ENST00000499624.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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.13232A>G		non_coding_transcript_exon_variant	2/2	1
GABPB1-AS1	ENST00000648591.1	n.449-1078A>G		intron_variant, non_coding_transcript_variant
GABPB1-AS1	ENST00000668321.1	n.87-1080A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41707 AN: 152046 Hom.: 7156 Cov.: 32

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.250 AC: 5 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.274 AC: 41710 AN: 152164 Hom.: 7155 Cov.: 32 AF XY: 0.281 AC XY: 20933 AN XY: 74382

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.304

Alfa AF: 0.290 Hom.: 1665

Bravo AF: 0.249

Asia WGS AF: 0.297 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.9
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17431095; hg19: chr15-50661449;