11-94665035-A-T

Variant names:

• chr11-94665035-A-T
• rs4127396
• ENST00000536540.5:n.437+10601T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000536540.5(PIWIL4-AS1):​n.437+10601T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: PIWIL4-AS1 ENST00000536540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIWIL4-AS1	NR_135093.1	n.523+10601T>A		intron_variant	Intron 4 of 4
PIWIL4-AS1	NR_135094.1	n.436+10601T>A		intron_variant	Intron 3 of 3
PIWIL4-AS1	NR_135096.1	n.523+10601T>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIWIL4-AS1	ENST00000536540.5	n.437+10601T>A		intron_variant	Intron 4 of 4	3
PIWIL4-AS1	ENST00000537874.1	n.436+10601T>A		intron_variant	Intron 3 of 3	4
PIWIL4-AS1	ENST00000767899.1	n.508+10601T>A		intron_variant	Intron 4 of 4
PIWIL4-AS1	ENST00000767901.1	n.556+10601T>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 4429

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	0.72
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4127396; hg19: chr11-94398201;