12-3906132-C-G

Variant names:

• chr12-3906132-C-G
• rs11609145
• ENST00000537149.2:n.416-3752C>G

Variant summary

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

The ENST00000537149.2(PARP11-AS1):​n.416-3752C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 135,136 control chromosomes in the GnomAD database, including 3,231 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 0.23 (3231 hom., cov: 29)
• Consequence: PARP11-AS1 ENST00000537149.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 1 publications found

Genes affected

PARP11-AS1 (HGNC:40103): (PARP11 antisense RNA 1)

ENSG00000288729 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537149.2. 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
	PARP11-AS1	NR_183432.1		n.1786-3752C>G		intron	N/A
	PARP11-AS1	NR_183433.1		n.138-3752C>G		intron	N/A
	PARP11-AS1	NR_183435.1		n.216+751C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARP11-AS1	ENST00000537149.2	TSL:3	n.416-3752C>G		intron	N/A
	PARP11-AS1	ENST00000545163.4	TSL:3	n.233+751C>G		intron	N/A
	PARP11-AS1	ENST00000545357.1	TSL:3	n.136-3752C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 30623 AN: 135030 Hom.: 3226 Cov.: 29

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.227 AC: 30655 AN: 135136 Hom.: 3231 Cov.: 29 AF XY: 0.224 AC XY: 14727 AN XY: 65696

African (AFR) AF: 0.266 AC: 10277 AN: 38658

American (AMR) AF: 0.171 AC: 2083 AN: 12192

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 626 AN: 3172

East Asian (EAS) AF: 0.0158 AC: 71 AN: 4490

South Asian (SAS) AF: 0.163 AC: 718 AN: 4406

European-Finnish (FIN) AF: 0.238 AC: 2082 AN: 8760

Middle Eastern (MID) AF: 0.232 AC: 59 AN: 254

European-Non Finnish (NFE) AF: 0.233 AC: 14130 AN: 60526

Other (OTH) AF: 0.211 AC: 390 AN: 1844

Alfa AF: 0.198 Hom.: 348

Bravo AF: 0.201

Asia WGS AF: 0.0940 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.80
PhyloP100		-0.32

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: rs11609145;

hg19: chr12-4015298;