12-90114532-G-T

Variant names:

• chr12-90114532-G-T
• rs10777224
• ENST00000716130.1:n.653+13691G>T

Variant summary

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

The ENST00000716130.1(ATP2B1-AS1):​n.653+13691G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,054 control chromosomes in the GnomAD database, including 41,958 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 0.74 (41958 hom., cov: 31)
• Consequence: ATP2B1-AS1 ENST00000716130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2B1-AS1	ENST00000716130.1	n.653+13691G>T		intron_variant	Intron 6 of 7
ATP2B1-AS1	ENST00000716133.1	n.397+6711G>T		intron_variant	Intron 4 of 5
ATP2B1-AS1	ENST00000716135.1	n.602+6711G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111707 AN: 151936 Hom.: 41940 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.735 AC: 111771 AN: 152054 Hom.: 41958 Cov.: 31 AF XY: 0.741 AC XY: 55056 AN XY: 74322

African (AFR) AF: 0.574 AC: 23785 AN: 41450

American (AMR) AF: 0.710 AC: 10835 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2918 AN: 3466

East Asian (EAS) AF: 0.877 AC: 4514 AN: 5150

South Asian (SAS) AF: 0.825 AC: 3976 AN: 4820

European-Finnish (FIN) AF: 0.847 AC: 8979 AN: 10596

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54247 AN: 67990

Other (OTH) AF: 0.745 AC: 1570 AN: 2108

Alfa AF: 0.781 Hom.: 22853

Bravo AF: 0.716

Asia WGS AF: 0.791 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10777224; hg19: chr12-90508309;