rs10858946

Variant names:

• chr12-90050265-A-C
• rs10858946
• ENST00000549551.2:n.293-50438A>C

Variant summary

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

The ENST00000549551.2(ATP2B1-AS1):​n.293-50438A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,102 control chromosomes in the GnomAD database, including 4,246 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 0.21 (4246 hom., cov: 31)
• Consequence: ATP2B1-AS1 ENST00000549551.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369890	XR_001749246.2	n.1019-16731A>C		intron_variant	Intron 8 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2B1-AS1	ENST00000549551.2	n.293-50438A>C		intron_variant	Intron 3 of 5	5
ATP2B1-AS1	ENST00000651272.1	n.571-44171A>C		intron_variant	Intron 5 of 6
ATP2B1-AS1	ENST00000716130.1	n.514+28709A>C		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32119 AN: 151984 Hom.: 4244 Cov.: 31

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.211 AC: 32125 AN: 152102 Hom.: 4246 Cov.: 31 AF XY: 0.209 AC XY: 15569 AN XY: 74350

African (AFR) AF: 0.0555 AC: 2305 AN: 41518

American (AMR) AF: 0.197 AC: 3011 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3472

East Asian (EAS) AF: 0.122 AC: 630 AN: 5180

South Asian (SAS) AF: 0.151 AC: 724 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3606 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20208 AN: 67966

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.247 Hom.: 644

Bravo AF: 0.193

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10858946; hg19: chr12-90444042;