rs12786215

Variant names:

• chr11-94650308-G-A
• rs12786215
• ENST00000536540.5:n.437+25328C>T

Variant summary

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

The ENST00000536540.5(PIWIL4-AS1):​n.437+25328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,158 control chromosomes in the GnomAD database, including 993 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 0.11 (993 hom., cov: 32)
• Consequence: PIWIL4-AS1 ENST00000536540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

Genes affected

PIWIL4-AS1 (HGNC:55493): (PIWIL4 antisense RNA 1)

LINC02700 (HGNC:54214): (long intergenic non-protein coding RNA 2700)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536540.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIWIL4-AS1	NR_135093.1		n.523+25328C>T		intron	N/A
	PIWIL4-AS1	NR_135094.1		n.436+25328C>T		intron	N/A
	PIWIL4-AS1	NR_135096.1		n.523+25328C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIWIL4-AS1	ENST00000536540.5	TSL:3	n.437+25328C>T		intron	N/A
	PIWIL4-AS1	ENST00000537874.1	TSL:4	n.436+25328C>T		intron	N/A
	LINC02700	ENST00000540151.6	TSL:3	n.842-166G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16856 AN: 152040 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.111 AC: 16867 AN: 152158 Hom.: 993 Cov.: 32 AF XY: 0.111 AC XY: 8257 AN XY: 74396

African (AFR) AF: 0.0865 AC: 3589 AN: 41486

American (AMR) AF: 0.0993 AC: 1519 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.138 AC: 712 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4818

European-Finnish (FIN) AF: 0.0686 AC: 727 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7935 AN: 68006

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.110 Hom.: 557

Bravo AF: 0.108

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.36
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12786215; hg19: chr11-94383474;