12-131929142-G-A

Position:

• chr12-131929142-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000539078.1(PUS1-AS1):​n.167+43C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.34 (2313 hom., cov: 11)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PUS1-AS1 ENST00000539078.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.2).
• BP6: Variant 12-131929142-G-A is Benign according to our data. Variant chr12-131929142-G-A is described in ClinVar as [Benign]. Clinvar id is 676228.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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+43C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 23663 AN: 70540 Hom.: 2311 Cov.: 11

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.289

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.324

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.335 AC: 23677 AN: 70588 Hom.: 2313 Cov.: 11 AF XY: 0.332 AC XY: 11550 AN XY: 34808

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.320

Alfa AF: 0.0197 Hom.: 9

Bravo AF: 0.170

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	0.27
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75594148; hg19: chr12-132413687;