ENST00000549551.2:n.293-50998A>G

Variant names:

• chr12-90049705-A-G
• rs10858945
• ENST00000549551.2:n.293-50998A>G

Variant summary

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

The ENST00000549551.2(ATP2B1-AS1):​n.293-50998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,840 control chromosomes in the GnomAD database, including 18,305 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 0.48 (18305 hom., cov: 30)
• Consequence: ATP2B1-AS1 ENST00000549551.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 19 publications found

Genes affected

ATP2B1-AS1 (HGNC:27883): (ATP2B1 antisense RNA 1)

LOC105369890 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369890	XR_001749246.2	n.1019-17291A>G		intron_variant	Intron 8 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2B1-AS1	ENST00000549551.2	n.293-50998A>G		intron_variant	Intron 3 of 5	5
ATP2B1-AS1	ENST00000651272.1	n.571-44731A>G		intron_variant	Intron 5 of 6
ATP2B1-AS1	ENST00000716130.1	n.514+28149A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73430 AN: 151722 Hom.: 18295 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.484 AC: 73465 AN: 151840 Hom.: 18305 Cov.: 30 AF XY: 0.484 AC XY: 35911 AN XY: 74206

African (AFR) AF: 0.568 AC: 23485 AN: 41322

American (AMR) AF: 0.390 AC: 5950 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3196 AN: 5172

South Asian (SAS) AF: 0.605 AC: 2904 AN: 4800

European-Finnish (FIN) AF: 0.380 AC: 4002 AN: 10542

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30408 AN: 67966

Other (OTH) AF: 0.489 AC: 1031 AN: 2108

Alfa AF: 0.465 Hom.: 73166

Bravo AF: 0.487

Asia WGS AF: 0.554 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10858945; hg19: chr12-90443482;