rs4127396

chr11-94665035-A-Gchr11-94665035-A-T

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+10601T>C 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 0.287 in 152,132 control chromosomes in the GnomAD database, including 6,728 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 0.29 (6728 hom., cov: 33)
• Consequence: PIWIL4-AS1 NR_135093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIWIL4-AS1	NR_135093.1	n.523+10601T>C		intron_variant, non_coding_transcript_variant
PIWIL4-AS1	NR_135094.1	n.436+10601T>C		intron_variant, non_coding_transcript_variant
PIWIL4-AS1	NR_135096.1	n.523+10601T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIWIL4-AS1	ENST00000536540.5	n.437+10601T>C		intron_variant, non_coding_transcript_variant		3
PIWIL4-AS1	ENST00000537874.1	n.436+10601T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43556 AN: 152014 Hom.: 6721 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.287 AC: 43588 AN: 152132 Hom.: 6728 Cov.: 33 AF XY: 0.285 AC XY: 21167 AN XY: 74384

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.0685

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.304

Alfa AF: 0.321 Hom.: 3945

Bravo AF: 0.282

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4127396; hg19: chr11-94398201;