rs8108419

chr19-48490583-G-A

Variant summary

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

The NM_001388485.1(LMTK3):c.4366+525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 149,626 control chromosomes in the GnomAD database, including 3,600 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 0.21 (3600 hom., cov: 30)
• Consequence: LMTK3 NM_001388485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMTK3	NM_001388485.1	c.4366+525C>T		intron_variant		ENST00000600059.6
LMTK3	NM_001080434.2	c.4366+525C>T		intron_variant
LMTK3	XM_011526411.3	c.4444+525C>T		intron_variant
LMTK3	XM_011526412.3	c.4411+525C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMTK3	ENST00000600059.6	c.4366+525C>T		intron_variant		2	NM_001388485.1	P2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 31821 AN: 149550 Hom.: 3600 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.216

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.213 AC: 31838 AN: 149626 Hom.: 3600 Cov.: 30 AF XY: 0.216 AC XY: 15756 AN XY: 72864

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.226

Alfa AF: 0.223 Hom.: 3931

Bravo AF: 0.201

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.17
Dann	Benign	0.81

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: rs8108419; hg19: chr19-48993840;