chr15-50369252-A-G

Variant names:

• chr15-50369252-A-G
• rs17431095
• ENST00000499624.4:n.13743A>G

Variant summary

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

The ENST00000499624.4(GABPB1-AS1):​n.13743A>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 ENST00000499624.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 3 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=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABPB1-AS1	ENST00000499624.4	n.13743A>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
GABPB1-AS1	ENST00000648591.1	n.449-1078A>G		intron_variant	Intron 2 of 2
GABPB1-AS1	ENST00000668321.2	n.87-1080A>G		intron_variant	Intron 1 of 1

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

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) AF: 0.222 AC: 4 AN: 18

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.0727 AC: 3022 AN: 41566

American (AMR) AF: 0.275 AC: 4193 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2175 AN: 5186

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4820

European-Finnish (FIN) AF: 0.467 AC: 4930 AN: 10548

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24131 AN: 67994

Other (OTH) AF: 0.304 AC: 643 AN: 2112

Alfa AF: 0.303 Hom.: 3062

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
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs17431095; hg19: chr15-50661449;