rs3923716

chr12-131927715-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539078.1(PUS1-AS1):n.395+248G>T 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 0.238 in 152,006 control chromosomes in the GnomAD database, including 7,387 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 0.24 (7387 hom., cov: 32)
• Consequence: PUS1-AS1 ENST00000539078.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PUS1-AS1	XR_001749414.2	n.393+248G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PUS1-AS1	ENST00000539078.1	n.395+248G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36111 AN: 151888 Hom.: 7372 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.238 AC: 36172 AN: 152006 Hom.: 7387 Cov.: 32 AF XY: 0.240 AC XY: 17828 AN XY: 74304

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.207

Alfa AF: 0.129 Hom.: 1101

Bravo AF: 0.248

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.6
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923716; hg19: chr12-132412260;