Variant chr3-42210085-CGGAGGA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BP6

The ENST00000341421.7(TRAK1):c.1916_1921del(p.Glu639_Glu640del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000803 in 1,539,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00086 ( 0 hom. )

Consequence

TRAK1
ENST00000341421.7 inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Variant links:

Genes affected

TRAK1 (HGNC:29947): (trafficking kinesin protein 1) Predicted to enable GABA receptor binding activity and myosin binding activity. Involved in endosome to lysosome transport. Located in early endosome and mitochondrion. Implicated in developmental and epileptic encephalopathy 68. [provided by Alliance of Genome Resources, Apr 2022]

TRAK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in ENST00000341421.7

BP6

Variant 3-42210085-CGGAGGA-C is Benign according to our data. Variant chr3-42210085-CGGAGGA-C is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAK1	NM_001042646.3 linkuse as main transcript	c.1963+127_1963+132del		intron_variant		ENST00000327628.10	NP_001036111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAK1	ENST00000327628.10 linkuse as main transcript	c.1963+127_1963+132del		intron_variant		1	NM_001042646.3	ENSP00000328998	P1	Q9UPV9-1

Frequencies

GnomAD3 genomes

AF:

0.000224

AC:

AN:

147388

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000751

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000879

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000437

Gnomad FIN

AF:

0.000204

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000195

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00282

AC:

535

AN:

189446

Hom.:

AF XY:

0.00324

AC XY:

332

AN XY:

102570

show subpopulations

Gnomad AFR exome

AF:

0.000691

Gnomad AMR exome

AF:

0.00129

Gnomad ASJ exome

AF:

0.00483

Gnomad EAS exome

AF:

0.000411

Gnomad SAS exome

AF:

0.00504

Gnomad FIN exome

AF:

0.00285

Gnomad NFE exome

AF:

0.00335

Gnomad OTH exome

AF:

0.00168

GnomAD4 exome

AF:

0.000864

AC:

1203

AN:

1391646

Hom.:

AF XY:

0.000991

AC XY:

685

AN XY:

691044

show subpopulations

Gnomad4 AFR exome

AF:

0.000499

Gnomad4 AMR exome

AF:

0.000959

Gnomad4 ASJ exome

AF:

0.00161

Gnomad4 EAS exome

AF:

0.0000770

Gnomad4 SAS exome

AF:

0.00226

Gnomad4 FIN exome

AF:

0.00105

Gnomad4 NFE exome

AF:

0.000768

Gnomad4 OTH exome

AF:

0.000866

GnomAD4 genome

AF:

0.000224

AC:

AN:

147480

Hom.:

Cov.:

AF XY:

0.000321

AC XY:

AN XY:

71610

show subpopulations

Gnomad4 AFR

AF:

0.0000749

Gnomad4 AMR

AF:

0.000878

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000438

Gnomad4 FIN

AF:

0.000204

Gnomad4 NFE

AF:

0.000195

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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