Variant 19-48493922-GTCC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BP6BS2

The NM_001388485.1(LMTK3):c.3861_3863delGGA(p.Glu1287del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00401 in 1,030,594 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0033 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0041 ( 11 hom. )

Consequence

LMTK3
NM_001388485.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.46

Variant links:

Genes affected

LMTK3 (HGNC:19295): (lemur tyrosine kinase 3) Predicted to enable protein kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in Golgi membrane; axon; and dendrite. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LMTK3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001388485.1

BP6

Variant 19-48493922-GTCC-G is Benign according to our data. Variant chr19-48493922-GTCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3042586.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMTK3	NM_001388485.1 linkuse as main transcript	c.3861_3863delGGA	p.Glu1287del	disruptive_inframe_deletion	12/15	ENST00000600059.6	NP_001375414.1
LMTK3	NM_001080434.2 linkuse as main transcript	c.3861_3863delGGA	p.Glu1287del	disruptive_inframe_deletion	13/16		NP_001073903.2
LMTK3	XM_011526411.3 linkuse as main transcript	c.3939_3941delGGA	p.Glu1313del	disruptive_inframe_deletion	13/16		XP_011524713.1	A0A3B3ISL5
LMTK3	XM_011526412.3 linkuse as main transcript	c.3906_3908delGGA	p.Glu1302del	disruptive_inframe_deletion	13/16		XP_011524714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMTK3	ENST00000600059.6 linkuse as main transcript	c.3861_3863delGGA	p.Glu1287del	disruptive_inframe_deletion	12/15	2	NM_001388485.1	ENSP00000472020.1		Q96Q04

Frequencies

GnomAD3 genomes

AF:

0.00325

AC:

480

AN:

147554

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000806

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00276

Gnomad ASJ

AF:

0.00236

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00996

Gnomad FIN

AF:

0.00235

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.00486

Gnomad OTH

AF:

0.00196

GnomAD3 exomes

AF:

0.00530

AC:

AN:

3018

Hom.:

AF XY:

0.00518

AC XY:

AN XY:

1738

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00769

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00562

Gnomad NFE exome

AF:

0.00604

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00414

AC:

3651

AN:

882932

Hom.:

AF XY:

0.00425

AC XY:

1763

AN XY:

414862

show subpopulations

Gnomad4 AFR exome

AF:

0.000300

Gnomad4 AMR exome

AF:

0.00112

Gnomad4 ASJ exome

AF:

0.00290

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0148

Gnomad4 FIN exome

AF:

0.00226

Gnomad4 NFE exome

AF:

0.00392

Gnomad4 OTH exome

AF:

0.00610

GnomAD4 genome

AF:

0.00325

AC:

480

AN:

147662

Hom.:

Cov.:

AF XY:

0.00298

AC XY:

214

AN XY:

71918

show subpopulations

Gnomad4 AFR

AF:

0.000804

Gnomad4 AMR

AF:

0.00276

Gnomad4 ASJ

AF:

0.00236

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00997

Gnomad4 FIN

AF:

0.00235

Gnomad4 NFE

AF:

0.00486

Gnomad4 OTH

AF:

0.00194

Alfa

AF:

0.000370

Hom.:

Bravo

AF:

0.00307

Asia WGS

AF:

0.00548

AC:

AN:

2936

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

LMTK3-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 21, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over