12-79935553-A-C

Position:

• chr12-79935553-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NR_146535.1(PPP1R12A-AS1):​n.273A>C variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00914 in 985,758 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.010 (25 hom., cov: 33)
  • Exomes 𝑓: 0.0090 (31 hom.)
• Consequence: PPP1R12A-AS1 NR_146535.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.106

Genes affected

PPP1R12A-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 12-79935553-A-C is Benign according to our data. Variant chr12-79935553-A-C is described in ClinVar as [Benign]. Clinvar id is 2643190.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R12A-AS1	NR_146533.1	n.273A>C		non_coding_transcript_exon_variant	1/3
PPP1R12A-AS1	NR_146534.1	n.273A>C		non_coding_transcript_exon_variant	1/2
PPP1R12A-AS1	NR_146535.1	n.273A>C		splice_region_variant, non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R12A-AS1	ENST00000552885.2	n.653A>C		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1545 AN: 152154 Hom.: 25 Cov.: 33

Gnomad AFR AF: 0.00150

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00360

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.00622

GnomAD4 exome AF: 0.00896 AC: 7467 AN: 833486 Hom.: 31 Cov.: 31 AF XY: 0.00888 AC XY: 3417 AN XY: 384986

Gnomad4 AFR exome AF: 0.00127

Gnomad4 AMR exome AF: 0.00606

Gnomad4 ASJ exome AF: 0.00775

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000181

Gnomad4 FIN exome AF: 0.0310

Gnomad4 NFE exome AF: 0.00944

Gnomad4 OTH exome AF: 0.00688

GnomAD4 genome AF: 0.0101 AC: 1545 AN: 152272 Hom.: 25 Cov.: 33 AF XY: 0.0118 AC XY: 881 AN XY: 74464

Gnomad4 AFR AF: 0.00149

Gnomad4 AMR AF: 0.00360

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.00616

Alfa AF: 0.0122 Hom.: 1

Bravo AF: 0.00575

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2023

PPP1R12A: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76824425; hg19: chr12-80329333;