dbSNP rs16966334: PATL2:c.-240G>C (chr15-44710916-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387263.1(PATL2):c.-240G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 151,598 control chromosomes in the GnomAD database, including 384 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 0.054 ( 359 hom., cov: 29)

Exomes 𝑓: 0.058 ( 25 hom. )

Consequence

PATL2
NM_001387263.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301

Publications

5 publications found

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 Gene-Disease associations (from GenCC):

oocyte maturation defect 4
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

PATL2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PATL2	NM_001387263.1 link	c.-240G>C		5_prime_UTR_variant	Exon 2 of 18	ENST00000682850.1	NP_001374192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PATL2	ENST00000682850.1 link	c.-240G>C		5_prime_UTR_variant	Exon 2 of 18		NM_001387263.1	ENSP00000508024.1
PATL2	ENST00000558573.1 link	n.297+104G>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0537

AC:

7841

AN:

146064

Hom.:

361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0782

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.00347

Gnomad NFE

AF:

0.0221

Gnomad OTH

AF:

0.0465

GnomAD4 exome

AF:

0.0578

AC:

314

AN:

5428

Hom.:

AF XY:

0.0631

AC XY:

194

AN XY:

3074

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.117

AC:

124

AN:

1060

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.133

AC:

AN:

150

South Asian (SAS)

AF:

0.0817

AC:

126

AN:

1542

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0161

AC:

AN:

2428

Other (OTH)

AF:

0.0309

AC:

AN:

162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0537

AC:

7853

AN:

146170

Hom.:

359

Cov.:

AF XY:

0.0551

AC XY:

3892

AN XY:

70692

show subpopulations

African (AFR)

AF:

0.0783

AC:

3108

AN:

39696

American (AMR)

AF:

0.106

AC:

1494

AN:

14126

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

102

AN:

3432

East Asian (EAS)

AF:

0.186

AC:

894

AN:

4818

South Asian (SAS)

AF:

0.124

AC:

565

AN:

4564

European-Finnish (FIN)

AF:

0.0122

AC:

114

AN:

9316

Middle Eastern (MID)

AF:

0.00376

AC:

AN:

266

European-Non Finnish (NFE)

AF:

0.0221

AC:

1479

AN:

67028

Other (OTH)

AF:

0.0475

AC:

AN:

2022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

338

676

1015

1353

1691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0410

Hom.:

Bravo

AF:

0.0615

Asia WGS

AF:

0.135

AC:

468

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.7

(source)

DANN

Benign

0.75

PhyloP100

-0.30

PromoterAI

-0.041

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over