rs1055746

Variant names:

• chr15-52551073-A-C
• rs1055746
• NM_006628.6:c.*861T>G

Variant summary

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

The NM_006628.6(ARPP19):​c.*861T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,688 control chromosomes in the GnomAD database, including 887 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 0.10 (886 hom., cov: 33)
  • Exomes 𝑓: 0.060 (1 hom.)
• Consequence: ARPP19 NM_006628.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 10 publications found

Genes affected

ARPP19 (HGNC:16967): (cAMP regulated phosphoprotein 19) The 19-kD cAMP-regulated phosphoprotein plays a role in regulating mitosis by inhibiting protein phosphatase-2A (PP2A; see MIM 176915) (summary by Gharbi-Ayachi et al., 2010 [PubMed 21164014]).[supplied by OMIM, Feb 2011]

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 = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARPP19	NM_006628.6	c.*861T>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000249822.9	NP_006619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARPP19	ENST00000249822.9	c.*861T>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_006628.6	ENSP00000249822.4
ARPP19	ENST00000566423.5	c.*861T>G		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000455625.1
ARPP19	ENST00000561650.5	c.*861T>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000454234.1
ARPP19	ENST00000568196.1	c.*861T>G		downstream_gene_variant		2		ENSP00000457805.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15610 AN: 152140 Hom.: 887 Cov.: 33

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.0605 AC: 26 AN: 430 Hom.: 1 Cov.: 0 AF XY: 0.0577 AC XY: 15 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0590 AC: 25 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.102 AC: 15601 AN: 152258 Hom.: 886 Cov.: 33 AF XY: 0.0971 AC XY: 7233 AN XY: 74460

African (AFR) AF: 0.0886 AC: 3679 AN: 41534

American (AMR) AF: 0.107 AC: 1638 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0847 AC: 409 AN: 4826

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10606

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

European-Non Finnish (NFE) AF: 0.123 AC: 8338 AN: 68016

Other (OTH) AF: 0.125 AC: 265 AN: 2114

Alfa AF: 0.116 Hom.: 464

Bravo AF: 0.107

Asia WGS AF: 0.0390 AC: 137 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.85
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1055746; hg19: chr15-52843270;