X-15415414-T-C

Position:

• chrX-15415414-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001018109.3(PIR):​c.566-7864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.66 (17363 hom., 21089 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: PIR NM_001018109.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

Genes affected

PIR (HGNC:30048): (pirin) This gene encodes a member of the cupin superfamily. The encoded protein is an Fe(II)-containing nuclear protein expressed in all tissues of the body and concentrated within dot-like subnuclear structures. Interactions with nuclear factor I/CCAAT box transcription factor as well as B cell lymphoma 3-encoded oncoprotein suggest the encoded protein may act as a transcriptional cofactor and be involved in the regulation of DNA transcription and replication. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008]

PIR-FIGF (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIR	NM_001018109.3	c.566-7864A>G		intron_variant		ENST00000380420.10	NP_001018119.1
PIR	NM_003662.4	c.566-7864A>G		intron_variant			NP_003653.1
PIR-FIGF	NR_037859.2	n.618-7864A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIR	ENST00000380420.10	c.566-7864A>G		intron_variant		1	NM_001018109.3	ENSP00000369785.5
PIR	ENST00000380421.3	c.566-7864A>G		intron_variant		1		ENSP00000369786.3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 72504 AN: 110149 Hom.: 17368 Cov.: 23 AF XY: 0.650 AC XY: 21065 AN XY: 32387

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.652

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.658 AC: 72518 AN: 110200 Hom.: 17363 Cov.: 23 AF XY: 0.650 AC XY: 21089 AN XY: 32448

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.655

Alfa AF: 0.700 Hom.: 5395

Bravo AF: 0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs5935970; hg19: chrX-15433536;