rs10779614

chr1-214416571-A-Gchr1-214416571-A-T

Variant summary

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

The NM_005401.5(PTPN14):c.345-1845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,024 control chromosomes in the GnomAD database, including 41,731 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 0.74 (41731 hom., cov: 31)
• Consequence: PTPN14 NM_005401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.29

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN14	NM_005401.5	c.345-1845T>C		intron_variant		ENST00000366956.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN14	ENST00000366956.10	c.345-1845T>C		intron_variant		1	NM_005401.5	P1
PTPN14	ENST00000543945.5	c.345-1845T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112491 AN: 151906 Hom.: 41701 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.741 AC: 112574 AN: 152024 Hom.: 41731 Cov.: 31 AF XY: 0.740 AC XY: 54944 AN XY: 74288

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.709

Alfa AF: 0.747 Hom.: 85867

Bravo AF: 0.739

Asia WGS AF: 0.717 AC: 2494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.099
Dann	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs10779614; hg19: chr1-214589914;