rs3825427

Variant names:

• chr13-99196717-C-A
• rs3825427
• ENST00000445737.2:n.1159G>T

Variant summary

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

The ENST00000445737.2(UBAC2-AS1):​n.1159G>T 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 0.135 in 152,188 control chromosomes in the GnomAD database, including 1,622 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 0.14 (1622 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: UBAC2-AS1 ENST00000445737.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2-AS1	NR_036531.1		n.1478G>T		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	NR_036532.1		n.1204G>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2-AS1	ENST00000445737.2	TSL:1	n.1159G>T		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	ENST00000426037.9	TSL:2	n.1491G>T		non_coding_transcript_exon	Exon 2 of 2
	UBAC2-AS1	ENST00000658188.1		n.1422G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20577 AN: 152070 Hom.: 1615 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.140

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.135 AC: 20596 AN: 152188 Hom.: 1622 Cov.: 32 AF XY: 0.138 AC XY: 10304 AN XY: 74406

African (AFR) AF: 0.125 AC: 5174 AN: 41518

American (AMR) AF: 0.208 AC: 3179 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5178

South Asian (SAS) AF: 0.173 AC: 832 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7687 AN: 68002

Other (OTH) AF: 0.141 AC: 299 AN: 2116

Alfa AF: 0.128 Hom.: 511

Bravo AF: 0.142

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.25
PhyloP100		-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3825427;

hg19: chr13-99848971;