NM_152431.3:c.*321C>T

Variant names:

• chr11-94621313-C-T
• rs508485
• NM_152431.3:c.*321C>T

Variant summary

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

The NM_152431.3(PIWIL4):​c.*321C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 227,546 control chromosomes in the GnomAD database, including 27,801 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 0.49 (17936 hom., cov: 32)
  • Exomes 𝑓: 0.51 (9865 hom.)
• Consequence: PIWIL4 NM_152431.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 22 publications found

Genes affected

PIWIL4 (HGNC:18444): (piwi like RNA-mediated gene silencing 4) PIWIL4 belongs to the Argonaute family of proteins, which function in development and maintenance of germline stem cells (Sasaki et al., 2003 [PubMed 12906857]).[supplied by OMIM, Mar 2008]

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152431.3. 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	NM_152431.3	MANE Select	c.*321C>T		3_prime_UTR	Exon 20 of 20	NP_689644.2
	PIWIL4-AS1	NR_135093.1		n.523+54323G>A		intron	N/A
	PIWIL4-AS1	NR_135094.1		n.436+54323G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIWIL4	ENST00000299001.11	TSL:1 MANE Select	c.*321C>T		3_prime_UTR	Exon 20 of 20	ENSP00000299001.6
	PIWIL4	ENST00000446230.6	TSL:2	n.*1636C>T		non_coding_transcript_exon	Exon 19 of 19	ENSP00000413838.2
	PIWIL4	ENST00000446230.6	TSL:2	n.*1636C>T		3_prime_UTR	Exon 19 of 19	ENSP00000413838.2

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73807 AN: 151836 Hom.: 17920 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.492

GnomAD4 exome AF: 0.511 AC: 38661 AN: 75592 Hom.: 9865 Cov.: 0 AF XY: 0.509 AC XY: 19830 AN XY: 38994

African (AFR) AF: 0.475 AC: 1105 AN: 2328

American (AMR) AF: 0.483 AC: 1684 AN: 3490

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1406 AN: 2518

East Asian (EAS) AF: 0.489 AC: 2121 AN: 4340

South Asian (SAS) AF: 0.466 AC: 2853 AN: 6116

European-Finnish (FIN) AF: 0.539 AC: 2058 AN: 3820

Middle Eastern (MID) AF: 0.596 AC: 217 AN: 364

European-Non Finnish (NFE) AF: 0.517 AC: 24756 AN: 47920

Other (OTH) AF: 0.524 AC: 2461 AN: 4696

GnomAD4 genome AF: 0.486 AC: 73866 AN: 151954 Hom.: 17936 Cov.: 32 AF XY: 0.485 AC XY: 36058 AN XY: 74272

African (AFR) AF: 0.455 AC: 18836 AN: 41414

American (AMR) AF: 0.486 AC: 7425 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2447 AN: 5182

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5297 AN: 10534

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34098 AN: 67958

Other (OTH) AF: 0.493 AC: 1043 AN: 2114

Alfa AF: 0.494 Hom.: 47058

Bravo AF: 0.486

Asia WGS AF: 0.465 AC: 1619 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		0.039
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs508485; hg19: chr11-94354479;