rs10777211

Variant names:

• chr12-89932155-G-A
• rs10777211
• ENST00000547370.5:n.331-3667G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-89932155-G-A
• chr12-89932155-G-C

Variant summary

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

The ENST00000547370.5(ATP2B1-AS1):​n.331-3667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,894 control chromosomes in the GnomAD database, including 5,580 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 0.25 (5580 hom., cov: 32)
• Consequence: ATP2B1-AS1 ENST00000547370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547370.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP2B1-AS1	ENST00000547370.5	TSL:4	n.331-3667G>A		intron	N/A
	ATP2B1-AS1	ENST00000549551.2	TSL:5	n.226+10986G>A		intron	N/A
	ATP2B1-AS1	ENST00000651272.1		n.504+10986G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38354 AN: 151776 Hom.: 5583 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.252 AC: 38343 AN: 151894 Hom.: 5580 Cov.: 32 AF XY: 0.256 AC XY: 18990 AN XY: 74240

African (AFR) AF: 0.182 AC: 7532 AN: 41488

American (AMR) AF: 0.243 AC: 3708 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1103 AN: 3462

East Asian (EAS) AF: 0.574 AC: 2970 AN: 5176

South Asian (SAS) AF: 0.517 AC: 2496 AN: 4824

European-Finnish (FIN) AF: 0.149 AC: 1575 AN: 10576

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18164 AN: 67816

Other (OTH) AF: 0.274 AC: 576 AN: 2106

Alfa AF: 0.278 Hom.: 3316

Bravo AF: 0.254

Asia WGS AF: 0.466 AC: 1618 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs10777211; hg19: chr12-90325932;