rs1411875

Variant names:

• chr10-16485891-C-G
• rs1411875
• NM_001261836.2:c.433-461C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001261836.2(PTER):​c.433-461C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,852 control chromosomes in the GnomAD database, including 9,694 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 0.35 (9694 hom., cov: 31)
• Consequence: PTER NM_001261836.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001261836.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTER	NM_001261836.2	MANE Select	c.433-461C>G		intron	N/A	NP_001248765.1
	PTER	NM_001001484.3		c.433-461C>G		intron	N/A	NP_001001484.1
	PTER	NM_030664.5		c.433-461C>G		intron	N/A	NP_109589.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTER	ENST00000535784.7	TSL:1 MANE Select	c.433-461C>G		intron	N/A	ENSP00000439485.1
	PTER	ENST00000378000.5	TSL:1	c.433-461C>G		intron	N/A	ENSP00000367239.1
	PTER	ENST00000298942.4	TSL:5	c.433-461C>G		intron	N/A	ENSP00000298942.4

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53701 AN: 151734 Hom.: 9681 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.393

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53746 AN: 151852 Hom.: 9694 Cov.: 31 AF XY: 0.356 AC XY: 26399 AN XY: 74178

African (AFR) AF: 0.304 AC: 12573 AN: 41364

American (AMR) AF: 0.356 AC: 5435 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2324 AN: 5154

South Asian (SAS) AF: 0.476 AC: 2283 AN: 4798

European-Finnish (FIN) AF: 0.314 AC: 3316 AN: 10556

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24988 AN: 67944

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.353 Hom.: 1244

Bravo AF: 0.353

Asia WGS AF: 0.416 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1411875; hg19: chr10-16527890;