rs9517644

Variant names:

• chr13-99194645-T-C
• rs9517644
• ENST00000662755.1:n.375+2903A>G

Variant summary

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

The ENST00000662755.1(UBAC2-AS1):​n.375+2903A>G variant causes a intron 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 ENST00000662755.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAC2-AS1	ENST00000662755.1	n.375+2903A>G		intron_variant	Intron 2 of 2
UBAC2-AS1	ENST00000668596.1	n.323+2903A>G		intron_variant	Intron 2 of 3
UBAC2-AS1	ENST00000671580.1	n.583+2903A>G		intron_variant	Intron 2 of 3

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;