rs3825427

Positions:

• chr13-99196717-C-A

Variant summary

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

The NR_036531.1(UBAC2-AS1):​n.1478G>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 0.135 in 152,188 control chromosomes in the GnomAD database, including 1,622 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 0.14 (1622 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: UBAC2-AS1 NR_036531.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896

Genes affected

UBAC2-AS1 (HGNC:42502): (UBAC2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAC2-AS1	NR_036531.1	n.1478G>T		non_coding_transcript_exon_variant	2/2
UBAC2-AS1	NR_036532.1	n.1204G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAC2-AS1	ENST00000671580.1	n.583+831G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20577 AN: 152070 Hom.: 1615 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.140

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: 0.135 AC: 20596 AN: 152188 Hom.: 1622 Cov.: 32 AF XY: 0.138 AC XY: 10304 AN XY: 74406

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.141

Alfa AF: 0.137 Hom.: 335

Bravo AF: 0.142

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825427; hg19: chr13-99848971;