Variant 11-59655677-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_152716.3(PATL1):c.877C>T(p.Leu293Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00552 in 1,605,500 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0057 ( 29 hom. )

Consequence

PATL1
NM_152716.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.68

Variant links:

Genes affected

PATL1 (HGNC:26721): (PAT1 homolog 1, processing body mRNA decay factor) Enables poly(G) binding activity and poly(U) RNA binding activity. Involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Located in P-body and cytosol. Colocalizes with CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]

PATL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011297911).

BP6

Variant 11-59655677-G-A is Benign according to our data. Variant chr11-59655677-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 771889.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 585 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATL1	NM_152716.3 linkuse as main transcript	c.877C>T	p.Leu293Phe	missense_variant	8/19	ENST00000300146.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATL1	ENST00000300146.10 linkuse as main transcript	c.877C>T	p.Leu293Phe	missense_variant	8/19	1	NM_152716.3	P1	Q86TB9-1

Frequencies

GnomAD3 genomes

AF:

0.00386

AC:

587

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00327

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00638

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00401

AC:

942

AN:

235168

Hom.:

AF XY:

0.00408

AC XY:

518

AN XY:

127102

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00273

Gnomad ASJ exome

AF:

0.00532

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00207

Gnomad FIN exome

AF:

0.000627

Gnomad NFE exome

AF:

0.00642

Gnomad OTH exome

AF:

0.00448

GnomAD4 exome

AF:

0.00570

AC:

8285

AN:

1453264

Hom.:

Cov.:

AF XY:

0.00554

AC XY:

4000

AN XY:

721930

show subpopulations

Gnomad4 AFR exome

AF:

0.00144

Gnomad4 AMR exome

AF:

0.00297

Gnomad4 ASJ exome

AF:

0.00562

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00264

Gnomad4 FIN exome

AF:

0.00110

Gnomad4 NFE exome

AF:

0.00655

Gnomad4 OTH exome

AF:

0.00565

GnomAD4 genome

AF:

0.00384

AC:

585

AN:

152236

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

268

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00327

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000566

Gnomad4 NFE

AF:

0.00637

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00636

Hom.:

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00102

AC:

ESP6500EA

AF:

0.00652

AC:

ExAC

AF:

0.00369

AC:

446

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jun 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.027

Eigen

Benign

-0.025

Eigen_PC

Benign

0.010

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.66

M_CAP

Benign

0.013

MetaRNN

Benign

0.011

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.3

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.94

REVEL

Benign

0.16

Sift

Benign

0.075

Sift4G

Benign

0.70

Polyphen

0.86

Vest4

0.44

MVP

0.41

MPC

0.82

ClinPred

0.030

GERP RS

2.9

Varity_R

0.071

gMVP

0.14

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