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 ENST00000828047.1(PUS1-AS1):​n.354+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 ENST00000828047.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828047.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUS1-AS1	ENST00000539078.2	TSL:5	n.690+248G>T		intron	N/A
	PUS1-AS1	ENST00000828047.1		n.354+248G>T		intron	N/A
	PUS1-AS1	ENST00000828048.1		n.770+248G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3923716;

hg19: chr12-132412260;