rs2078139

Variant names:

• chr15-50367637-C-T
• rs2078139
• ENST00000499624.4:n.12128C>T

Variant summary

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

The ENST00000499624.4(GABPB1-AS1):​n.12128C>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 ENST00000499624.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 4 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=-0.94).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1-AS1	ENST00000499624.4	n.12128C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
GABPB1-AS1	ENST00000648591.1	n.449-2693C>T		intron_variant	Intron 2 of 2
GABPB1-AS1	ENST00000668321.2	n.87-2695C>T		intron_variant	Intron 1 of 1

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

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

African (AFR) AF: 0.150 AC: 6175 AN: 41302

American (AMR) AF: 0.276 AC: 4195 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1414 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1848 AN: 5156

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4812

European-Finnish (FIN) AF: 0.209 AC: 2158 AN: 10340

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13781 AN: 67870

Other (OTH) AF: 0.242 AC: 511 AN: 2108

Alfa AF: 0.205 Hom.: 508

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2078139; hg19: chr15-50659834;