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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PATL2	NM_001387263.1	MANE Select	c.-240G>C	5_prime_UTR	Exon 2 of 18	NP_001374192.1	C9JE40
PATL2	NM_001387262.1		c.-240G>C	5_prime_UTR	Exon 1 of 17	NP_001374191.1	C9JE40
PATL2	NM_001387261.1		c.-76+104G>C	intron	N/A	NP_001374190.1	C9JE40

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PATL2	ENST00000682850.1	MANE Select	c.-240G>C	5_prime_UTR	Exon 2 of 18	ENSP00000508024.1	C9JE40
PATL2	ENST00000890225.1		c.-121G>C	5_prime_UTR	Exon 2 of 17	ENSP00000560284.1
PATL2	ENST00000941555.1		c.-233G>C	5_prime_UTR	Exon 3 of 19	ENSP00000611614.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over