chr15-44665812-A-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

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

1
8

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 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
BS2
High Homozygotes in GnomAdExome4 at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PATL2NM_001387263.1 linkuse as main transcriptc.*141T>A 3_prime_UTR_variant 18/18 ENST00000682850.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PATL2ENST00000682850.1 linkuse as main transcriptc.*141T>A 3_prime_UTR_variant 18/18 NM_001387263.1 A2

Frequencies

GnomAD3 genomes
AF:
0.00268
AC:
408
AN:
152172
Hom.:
0
Cov.:
32
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.:
1
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.:
10
Cov.:
30
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.:
0
Cov.:
32
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.:
0
Bravo
AF:
0.00276
TwinsUK
AF:
0.00431
AC:
16
ALSPAC
AF:
0.00415
AC:
16
ExAC
AF:
0.00146
AC:
32
Asia WGS
AF:
0.000289
AC:
1
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 submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.52
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
13
DANN
Benign
0.74
FATHMM_MKL
Benign
0.023
N
LIST_S2
Benign
0.15
T
MetaRNN
Benign
0.0039
T
MutationTaster
Benign
1.0
N;N;N
PROVEAN
Benign
-0.50
N
Sift
Pathogenic
0.0
D
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.

Other links and lift over

dbSNP: rs186338121; hg19: chr15-44958010; API