rs11069357

Positions:

• chr13-99197376-A-G

Variant summary

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

The NR_036531.1(UBAC2-AS1):​n.819T>C 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 0.577 in 152,034 control chromosomes in the GnomAD database, including 27,042 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 0.58 (27017 hom., cov: 30)
  • Exomes 𝑓: 0.73 (25 hom.)
• Consequence: UBAC2-AS1 NR_036531.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAC2-AS1	NR_036531.1	n.819T>C		non_coding_transcript_exon_variant	2/2
UBAC2-AS1	NR_036532.1	n.545T>C		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+172T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87674 AN: 151830 Hom.: 27006 Cov.: 30

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.578

GnomAD4 exome AF: 0.733 AC: 63 AN: 86 Hom.: 25 Cov.: 0 AF XY: 0.726 AC XY: 45 AN XY: 62

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.730

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.577 AC: 87724 AN: 151948 Hom.: 27017 Cov.: 30 AF XY: 0.570 AC XY: 42360 AN XY: 74268

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.577

Alfa AF: 0.639 Hom.: 4020

Bravo AF: 0.566

Asia WGS AF: 0.425 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11069357; hg19: chr13-99849630;