rs10858945

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 ENST00000651272.1(ATP2B1-AS1):​n.571-44731A>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 ENST00000651272.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651272.1. 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
	ATP2B1-AS1	ENST00000549551.2	TSL:5	n.293-50998A>G		intron	N/A
	ATP2B1-AS1	ENST00000651272.1		n.571-44731A>G		intron	N/A
	ATP2B1-AS1	ENST00000716130.1		n.514+28149A>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10858945;

hg19: chr12-90443482;