rs17192114

Variant names:

• chr12-89777661-T-G
• rs17192114
• ENST00000651272.1:n.360-23300T>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.360-23300T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,260 control chromosomes in the GnomAD database, including 1,393 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 0.12 (1393 hom., cov: 32)
• Consequence: ATP2B1-AS1 ENST00000651272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 4 publications found

Genes affected

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

ENSG00000296746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984543	XR_007063399.1	n.171-23300T>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2B1-AS1	ENST00000651272.1	n.360-23300T>G		intron_variant	Intron 2 of 6
ENSG00000296746	ENST00000741520.1	n.175+6050A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17941 AN: 152142 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.118 AC: 17944 AN: 152260 Hom.: 1393 Cov.: 32 AF XY: 0.120 AC XY: 8904 AN XY: 74444

African (AFR) AF: 0.0276 AC: 1146 AN: 41574

American (AMR) AF: 0.151 AC: 2312 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5186

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4828

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10588

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10796 AN: 68002

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.145 Hom.: 2822

Bravo AF: 0.111

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.37
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs17192114; hg19: chr12-90171438;