10-16513529-A-T

Position:

• chr10-16513529-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000535784.7(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 ENST00000535784.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PTER	NM_001261836.2	c.*2273A>T		3_prime_UTR_variant	5/5	ENST00000535784.7	NP_001248765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTER	ENST00000535784.7	c.*2273A>T		3_prime_UTR_variant	5/5	1	NM_001261836.2	ENSP00000439485	P1
PTER	ENST00000378000.5	c.*2273A>T		3_prime_UTR_variant	6/6	1		ENSP00000367239	P1
PTER	ENST00000298942.4	c.*2273A>T		3_prime_UTR_variant	3/3	5		ENSP00000298942
PTER	ENST00000423462.6	c.*2273A>T		3_prime_UTR_variant	4/4	3		ENSP00000389535

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90809 AN: 151822 Hom.: 28058 Cov.: 32

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.: 27 Cov.: 0 AF XY: 0.319 AC XY: 83 AN XY: 260

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.598 AC: 90878 AN: 151938 Hom.: 28077 Cov.: 32 AF XY: 0.587 AC XY: 43564 AN XY: 74252

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.599

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
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055340; hg19: chr10-16555528; COSMIC: COSV54347915; COSMIC: COSV54347915;