chr13-99197376-A-G

Variant names:

• chr13-99197376-A-G
• rs11069357
• ENST00000445737.2:n.500T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445737.2(UBAC2-AS1):​n.500T>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 ENST00000445737.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• 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=-0.96).
• 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: ENST00000445737.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2-AS1	NR_036531.1		n.819T>C		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	NR_036532.1		n.545T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2-AS1	ENST00000445737.2	TSL:1	n.500T>C		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	ENST00000426037.9	TSL:2	n.832T>C		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	ENST00000658188.1		n.763T>C		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.730 AC: 54 AN: 74

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.366 AC: 15157 AN: 41414

American (AMR) AF: 0.546 AC: 8334 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2581 AN: 5150

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4816

European-Finnish (FIN) AF: 0.629 AC: 6636 AN: 10544

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

European-Non Finnish (NFE) AF: 0.712 AC: 48375 AN: 67964

Other (OTH) AF: 0.577 AC: 1218 AN: 2112

Alfa AF: 0.628 Hom.: 4074

Bravo AF: 0.566

Asia WGS AF: 0.425 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs11069357; hg19: chr13-99849630;