Variant 15-44665812-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting

The NM_001387263.1(PATL2):c.*141T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,522,328 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0027 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0036 ( 10 hom. )

Consequence

PATL2
NM_001387263.1 3_prime_UTR

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.535

Variant links:

Genes affected

PATL2 (HGNC:33630): (PAT1 homolog 2) Predicted to enable RNA binding activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to act upstream of or within negative regulation of cytoplasmic mRNA processing body assembly. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PATL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039250255).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00268 (408/152290) while in subpopulation NFE AF= 0.00469 (319/68018). AF 95% confidence interval is 0.00427. There are 0 homozygotes in gnomad4. There are 185 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATL2	NM_001387263.1 linkuse as main transcript	c.*141T>A		3_prime_UTR_variant	18/18	ENST00000682850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATL2	ENST00000682850.1 linkuse as main transcript	c.*141T>A		3_prime_UTR_variant	18/18		NM_001387263.1	A2

Frequencies

GnomAD3 genomes

AF:

0.00268

AC:

408

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000676

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00314

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00469

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00226

AC:

291

AN:

128840

Hom.:

AF XY:

0.00225

AC XY:

156

AN XY:

69280

show subpopulations

Gnomad AFR exome

AF:

0.000848

Gnomad AMR exome

AF:

0.00178

Gnomad ASJ exome

AF:

0.000142

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000858

Gnomad FIN exome

AF:

0.000623

Gnomad NFE exome

AF:

0.00432

Gnomad OTH exome

AF:

0.00136

GnomAD4 exome

AF:

0.00358

AC:

4911

AN:

1370038

Hom.:

Cov.:

AF XY:

0.00340

AC XY:

2293

AN XY:

675086

show subpopulations

Gnomad4 AFR exome

AF:

0.000570

Gnomad4 AMR exome

AF:

0.00135

Gnomad4 ASJ exome

AF:

0.0000418

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000721

Gnomad4 FIN exome

AF:

0.000665

Gnomad4 NFE exome

AF:

0.00429

Gnomad4 OTH exome

AF:

0.00328

GnomAD4 genome

AF:

0.00268

AC:

408

AN:

152290

Hom.:

Cov.:

AF XY:

0.00248

AC XY:

185

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.000674

Gnomad4 AMR

AF:

0.00314

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00469

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00276

Hom.:

Bravo

AF:

0.00276

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00415

AC:

ExAC

AF:

0.00146

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.52

Cadd

Benign

Dann

Benign

0.74

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.15

MetaRNN

Benign

0.0039

MutationTaster

Benign

1.0

N;N;N

PROVEAN

Benign

-0.50

Sift

Pathogenic

0.0

MVP

0.18

GERP RS

0.51

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over