rs3923716

Variant names:

• chr12-131927715-C-A
• rs3923716
• ENST00000539078.2:n.690+248G>T

Variant summary

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

The ENST00000539078.2(PUS1-AS1):​n.690+248G>T variant causes a intron 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 ENST00000539078.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PUS1-AS1	XR_001749414.2	n.393+248G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PUS1-AS1	ENST00000539078.2	n.690+248G>T		intron_variant	Intron 2 of 2	5
PUS1-AS1	ENST00000828047.1	n.354+248G>T		intron_variant	Intron 2 of 2
PUS1-AS1	ENST00000828048.1	n.770+248G>T		intron_variant	Intron 2 of 2
PUS1-AS1	ENST00000828049.1	n.394+248G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.556 AC: 22985 AN: 41354

American (AMR) AF: 0.149 AC: 2279 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3472

East Asian (EAS) AF: 0.104 AC: 540 AN: 5182

South Asian (SAS) AF: 0.124 AC: 600 AN: 4830

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0941 AC: 6397 AN: 67960

Other (OTH) AF: 0.207 AC: 437 AN: 2114

Alfa AF: 0.129 Hom.: 1451

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
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs3923716; hg19: chr12-132412260;