chr1-214357735-GA-G

Position:

• chr1-214357735-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005401.5(PTPN14):​c.*186del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.42 (14374 hom., cov: 0)
  • Exomes 𝑓: 0.47 (38626 hom.)
• Consequence: PTPN14 NM_005401.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.30

Genes affected

PTPN14 (HGNC:9647): (protein tyrosine phosphatase non-receptor type 14) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal noncatalytic domain similar to that of band 4.1 superfamily cytoskeleton-associated proteins, which suggested the membrane or cytoskeleton localization of this protein. It appears to regulate lymphatic development in mammals, and a loss of function mutation has been found in a kindred with a lymphedema-choanal atresia. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-214357735-GA-G is Benign according to our data. Variant chr1-214357735-GA-G is described in ClinVar as [Benign]. Clinvar id is 1249681.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN14	NM_005401.5	c.*186del		3_prime_UTR_variant	19/19	ENST00000366956.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN14	ENST00000366956.10	c.*186del		3_prime_UTR_variant	19/19	1	NM_005401.5	P1
PTPN14	ENST00000543945.5			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63545 AN: 151864 Hom.: 14371 Cov.: 0

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.376

GnomAD4 exome AF: 0.468 AC: 155680 AN: 332462 Hom.: 38626 Cov.: 0 AF XY: 0.464 AC XY: 79415 AN XY: 171206

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.428

Gnomad4 ASJ exome AF: 0.338

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.388

Gnomad4 FIN exome AF: 0.545

Gnomad4 NFE exome AF: 0.511

Gnomad4 OTH exome AF: 0.442

GnomAD4 genome AF: 0.418 AC: 63571 AN: 151982 Hom.: 14374 Cov.: 0 AF XY: 0.415 AC XY: 30785 AN XY: 74268

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.378

Alfa AF: 0.482 Hom.: 2293

Bravo AF: 0.399

Asia WGS AF: 0.365 AC: 1274 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3830398; hg19: chr1-214531078;