Genetic Variant PTER:c.*2273A>T (chr10-16513529-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001261836.2(PTER):c.*2273A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,368 control chromosomes in the GnomAD database, including 28,104 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 0.60 ( 28077 hom., cov: 32)

Exomes 𝑓: 0.34 ( 27 hom. )

Consequence

PTER
NM_001261836.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0850

Publications

14 publications found

Variant links:

Genes affected

PTER (HGNC:9590): (phosphotriesterase related) Predicted to enable hydrolase activity, acting on ester bonds and zinc ion binding activity. Involved in epithelial cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

PTER links:

C1QL3 (HGNC:19359): (complement C1q like 3) Predicted to enable identical protein binding activity. Predicted to act upstream of or within regulation of synapse organization. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

C1QL3 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTER	NM_001261836.2 link	c.*2273A>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000535784.7	NP_001248765.1
C1QL3	NM_001010908.2 link	c.*999T>A		downstream_gene_variant		ENST00000298943.4	NP_001010908.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTER	ENST00000535784.7 link	c.*2273A>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_001261836.2	ENSP00000439485.1
C1QL3	ENST00000298943.4 link	c.*999T>A		downstream_gene_variant		1	NM_001010908.2	ENSP00000298943.3

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

90809

AN:

151822

Hom.:

28058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.578

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.557

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.337

AC:

145

AN:

430

Hom.:

Cov.:

AF XY:

0.319

AC XY:

AN XY:

260

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.340

AC:

144

AN:

424

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.598

AC:

90878

AN:

151938

Hom.:

28077

Cov.:

AF XY:

0.587

AC XY:

43564

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.757

AC:

31395

AN:

41494

American (AMR)

AF:

0.569

AC:

8683

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

1765

AN:

3470

East Asian (EAS)

AF:

0.505

AC:

2607

AN:

5166

South Asian (SAS)

AF:

0.579

AC:

2792

AN:

4822

European-Finnish (FIN)

AF:

0.364

AC:

3830

AN:

10524

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.557

AC:

37822

AN:

67906

Other (OTH)

AF:

0.599

AC:

1257

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1770

3540

5311

7081

8851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.563

Hom.:

2890

Bravo

AF:

0.624

Asia WGS

AF:

0.528

AC:

1838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.2

(source)

DANN

Benign

0.77

PhyloP100

-0.085

Mutation Taster

=100/0

polymorphism (auto)

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over