Variant chr7-98192898-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014916.4(LMTK2):c.2433G>A(p.Pro811=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,613,644 control chromosomes in the GnomAD database, including 199,093 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 0.37 ( 13468 hom., cov: 32)

Exomes 𝑓: 0.49 ( 185625 hom. )

Consequence

LMTK2
NM_014916.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Variant links:

Genes affected

LMTK2 (HGNC:17880): (lemur tyrosine kinase 2) The protein encoded by this gene belongs to the protein kinase superfamily and the protein tyrosine kinase family. It contains N-terminal transmembrane helices and a long C-terminal cytoplasmic tail with serine/threonine/tyrosine kinase activity. This protein interacts with several other proteins, such as Inhibitor-2 (Inh2), protein phosphatase-1 (PP1C), p35, and myosin VI. It phosporylates other proteins, and is itself also phosporylated when interacting with cyclin-dependent kinase 5 (cdk5)/p35 complex. This protein involves in nerve growth factor (NGF)-TrkA signalling, and also plays a critical role in endosomal membrane trafficking. Mouse studies suggested an essential role of this protein in spermatogenesis. [provided by RefSeq, Oct 2009]

LMTK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-1.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMTK2	NM_014916.4 linkuse as main transcript	c.2433G>A	p.Pro811=	synonymous_variant	11/14	ENST00000297293.6	NP_055731.2
LMTK2	XM_011515981.4 linkuse as main transcript	c.2427G>A	p.Pro809=	synonymous_variant	11/14		XP_011514283.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMTK2	ENST00000297293.6 linkuse as main transcript	c.2433G>A	p.Pro811=	synonymous_variant	11/14	1	NM_014916.4	ENSP00000297293	P1

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56774

AN:

151896

Hom.:

13469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.619

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.430

GnomAD3 exomes

AF:

0.402

AC:

100938

AN:

251372

Hom.:

24275

AF XY:

0.411

AC XY:

55821

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.244

Gnomad ASJ exome

AF:

0.591

Gnomad EAS exome

AF:

0.142

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.472

Gnomad NFE exome

AF:

0.545

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.487

AC:

712448

AN:

1461630

Hom.:

185625

Cov.:

AF XY:

0.483

AC XY:

351136

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.0972

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.587

Gnomad4 EAS exome

AF:

0.125

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.479

Gnomad4 NFE exome

AF:

0.539

Gnomad4 OTH exome

AF:

0.473

GnomAD4 genome

AF:

0.373

AC:

56758

AN:

152014

Hom.:

13468

Cov.:

AF XY:

0.364

AC XY:

27072

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.111

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.581

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.463

Gnomad4 NFE

AF:

0.538

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.511

Hom.:

29049

Bravo

AF:

0.361

Asia WGS

AF:

0.180

AC:

626

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.44

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over