rs11105468

Variant names:

• chr12-89935056-T-A
• rs11105468
• ENST00000547370.5:n.331-766T>A

Variant summary

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

The ENST00000547370.5(ATP2B1-AS1):​n.331-766T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,020 control chromosomes in the GnomAD database, including 4,912 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 (4912 hom., cov: 32)
• Consequence: ATP2B1-AS1 ENST00000547370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 9 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 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

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	ENST00000547370.5	TSL:4	n.331-766T>A		intron	N/A
	ATP2B1-AS1	ENST00000549551.2	TSL:5	n.226+13887T>A		intron	N/A
	ATP2B1-AS1	ENST00000651272.1		n.504+13887T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38174 AN: 151902 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.251 AC: 38193 AN: 152020 Hom.: 4912 Cov.: 32 AF XY: 0.246 AC XY: 18287 AN XY: 74296

African (AFR) AF: 0.229 AC: 9506 AN: 41462

American (AMR) AF: 0.211 AC: 3227 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3468

East Asian (EAS) AF: 0.128 AC: 659 AN: 5168

South Asian (SAS) AF: 0.132 AC: 635 AN: 4812

European-Finnish (FIN) AF: 0.323 AC: 3404 AN: 10554

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19176 AN: 67960

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.263 Hom.: 664

Bravo AF: 0.241

Asia WGS AF: 0.135 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11105468; hg19: chr12-90328833;