rs12786215

Positions:

• chr11-94650308-G-A

Variant summary

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

The NR_135093.1(PIWIL4-AS1):​n.523+25328C>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 0.111 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 NR_135093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

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

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIWIL4-AS1	NR_135093.1	n.523+25328C>T		intron_variant, non_coding_transcript_variant
LINC02700	XR_007062842.1	n.1659-166G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIWIL4-AS1	ENST00000536540.5	n.437+25328C>T		intron_variant, non_coding_transcript_variant		3
LINC02700	ENST00000648581.1	n.1282-166G>A		intron_variant, non_coding_transcript_variant
	ENST00000693361.2			upstream_gene_variant

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

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.125

Alfa AF: 0.108 Hom.: 247

Bravo AF: 0.108

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12786215; hg19: chr11-94383474;