chr13-99194645-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662755.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2-AS1	ENST00000662755.1		n.375+2903A>G		intron	N/A
	UBAC2-AS1	ENST00000668596.2		n.386+2903A>G		intron	N/A
	UBAC2-AS1	ENST00000671580.2		n.653+2903A>G		intron	N/A

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

African (AFR) AF: 0.366 AC: 15171 AN: 41414

American (AMR) AF: 0.546 AC: 8343 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2605 AN: 5178

South Asian (SAS) AF: 0.461 AC: 2219 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6626 AN: 10548

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48391 AN: 67984

Other (OTH) AF: 0.576 AC: 1214 AN: 2108

Alfa AF: 0.613 Hom.: 5235

Bravo AF: 0.566

Asia WGS AF: 0.423 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.31
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs9517644; hg19: chr13-99846899;