12-131929053-A-C

Position:

• chr12-131929053-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000539078.1(PUS1-AS1):​n.167+132T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,888 control chromosomes in the GnomAD database, including 2,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (2305 hom., cov: 31)
  • Exomes 𝑓: 0.082 (0 hom.)
• Consequence: PUS1-AS1 ENST00000539078.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.666

Genes affected

PUS1-AS1 (HGNC:40706): (PUS1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.2).
• BP6: Variant 12-131929053-A-C is Benign according to our data. Variant chr12-131929053-A-C is described in ClinVar as [Benign]. Clinvar id is 676197.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PUS1-AS1	ENST00000539078.1	n.167+132T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23180 AN: 151656 Hom.: 2306 Cov.: 31

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.0820 AC: 10 AN: 122 Hom.: 0 AF XY: 0.100 AC XY: 9 AN XY: 90

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0889

GnomAD4 genome AF: 0.153 AC: 23174 AN: 151766 Hom.: 2305 Cov.: 31 AF XY: 0.154 AC XY: 11385 AN XY: 74162

Gnomad4 AFR AF: 0.0760

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0625 Hom.: 105

Bravo AF: 0.159

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

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	7.3
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78255464; hg19: chr12-132413598;