rs4127396

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-94665035-A-G
• chr11-94665035-A-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+10601T>C variant causes a intron 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 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: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIWIL4-AS1	NR_135093.1		n.523+10601T>C		intron	N/A
	PIWIL4-AS1	NR_135094.1		n.436+10601T>C		intron	N/A
	PIWIL4-AS1	NR_135096.1		n.523+10601T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIWIL4-AS1	ENST00000536540.5	TSL:3	n.437+10601T>C		intron	N/A
	PIWIL4-AS1	ENST00000537874.1	TSL:4	n.436+10601T>C		intron	N/A
	PIWIL4-AS1	ENST00000767899.1		n.508+10601T>C		intron	N/A

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

African (AFR) AF: 0.206 AC: 8538 AN: 41526

American (AMR) AF: 0.314 AC: 4810 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3468

East Asian (EAS) AF: 0.0685 AC: 355 AN: 5182

South Asian (SAS) AF: 0.302 AC: 1451 AN: 4812

European-Finnish (FIN) AF: 0.295 AC: 3115 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22793 AN: 67968

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.321 Hom.: 4429

Bravo AF: 0.282

Asia WGS AF: 0.193 AC: 671 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	1.0
DANN	Benign	0.69
PhyloP100		-0.38

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: rs4127396;

hg19: chr11-94398201;