rs9517644

Positions:

• chr13-99194645-T-C

Variant summary

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

The ENST00000671580.1(UBAC2-AS1):​n.583+2903A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,998 control chromosomes in the GnomAD database, including 27,028 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 (27028 hom., cov: 31)
• Consequence: UBAC2-AS1 ENST00000671580.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

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=-1.0).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2-AS1	ENST00000671580.1	n.583+2903A>G		intron_variant, non_coding_transcript_variant
UBAC2-AS1	ENST00000662755.1	n.375+2903A>G		intron_variant, non_coding_transcript_variant
UBAC2-AS1	ENST00000668596.1	n.323+2903A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87729 AN: 151880 Hom.: 27019 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.577 AC: 87776 AN: 151998 Hom.: 27028 Cov.: 31 AF XY: 0.570 AC XY: 42391 AN XY: 74310

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.576

Alfa AF: 0.621 Hom.: 5180

Bravo AF: 0.566

Asia WGS AF: 0.423 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9517644; hg19: chr13-99846899;