chr12-79694798-T-C

Variant names:

• chr12-79694798-T-C
• rs12827748
• ENST00000551995.1:n.253+4402T>C

Variant summary

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

The ENST00000551995.1(PPP1R12A-AS2):​n.253+4402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,990 control chromosomes in the GnomAD database, including 23,606 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 0.50 (23606 hom., cov: 31)
• Consequence: PPP1R12A-AS2 ENST00000551995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 7 publications found

Genes affected

PPP1R12A-AS2 (HGNC:55456): (PPP1R12A antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R12A-AS2	NR_187531.1	n.365+4402T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R12A-AS2	ENST00000551995.1	n.253+4402T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76003 AN: 151872 Hom.: 23613 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.500 AC: 75990 AN: 151990 Hom.: 23606 Cov.: 31 AF XY: 0.503 AC XY: 37375 AN XY: 74264

African (AFR) AF: 0.126 AC: 5235 AN: 41462

American (AMR) AF: 0.601 AC: 9174 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2151 AN: 5168

South Asian (SAS) AF: 0.463 AC: 2227 AN: 4806

European-Finnish (FIN) AF: 0.733 AC: 7724 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46032 AN: 67962

Other (OTH) AF: 0.515 AC: 1088 AN: 2114

Alfa AF: 0.618 Hom.: 15598

Bravo AF: 0.473

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.83
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12827748; hg19: chr12-80088578;