Variant rs2279216 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014889.4(PITRM1):c.2917+145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 831,298 control chromosomes in the GnomAD database, including 27,138 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 0.20 ( 3898 hom., cov: 34)

Exomes 𝑓: 0.25 ( 23240 hom. )

Consequence

PITRM1
NM_014889.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.642

Variant links:

Genes affected

PITRM1 (HGNC:17663): (pitrilysin metallopeptidase 1) The protein encoded by this gene is an ATP-dependent metalloprotease that degrades post-cleavage mitochondrial transit peptides. The encoded protein binds zinc and can also degrade amyloid beta A4 protein, suggesting a possible role in Alzheimer's disease. [provided by RefSeq, Dec 2016]

PITRM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITRM1	NM_014889.4 linkuse as main transcript	c.2917+145C>T		intron_variant		ENST00000224949.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITRM1	ENST00000224949.9 linkuse as main transcript	c.2917+145C>T		intron_variant		1	NM_014889.4	P3	Q5JRX3-1

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31106

AN:

152026

Hom.:

3897

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.213

GnomAD4 exome

AF:

0.254

AC:

172754

AN:

679154

Hom.:

23240

Cov.:

AF XY:

0.255

AC XY:

93471

AN XY:

366628

show subpopulations

Gnomad4 AFR exome

AF:

0.0516

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.239

Gnomad4 EAS exome

AF:

0.214

Gnomad4 SAS exome

AF:

0.244

Gnomad4 FIN exome

AF:

0.226

Gnomad4 NFE exome

AF:

0.286

Gnomad4 OTH exome

AF:

0.245

GnomAD4 genome

AF:

0.204

AC:

31107

AN:

152144

Hom.:

3898

Cov.:

AF XY:

0.203

AC XY:

15124

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0547

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.264

Hom.:

11392

Bravo

AF:

0.195

Asia WGS

AF:

0.204

AC:

712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.5

DANN

Benign

0.70

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over