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rs10634555

chr3-42210085-CGGAGGAGGAGGAGGA-Cchr3-42210085-CGGAGGAGGAGGAGGA-CGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGAchr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The ENST00000341421.7(TRAK1):c.1907_1921del(p.Glu636_Glu640del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,577,352 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000019 ( 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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP3
?
    BP3 - In-frame deletions/insertions in a repetitive region without a known function
Nonframeshift variant in repetitive region in ENST00000341421.7

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAK1NM_001042646.3 linkuse as main transcriptc.1963+118_1963+132del intron_variant ENST00000327628.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAK1ENST00000327628.10 linkuse as main transcriptc.1963+118_1963+132del intron_variant 1 NM_001042646.3 P1Q9UPV9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000122
AC:
18
AN:
147430
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000450
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000189
AC:
27
AN:
1429922
Hom.:
0
AF XY:
0.0000183
AC XY:
13
AN XY:
710170
show subpopulations
Gnomad4 AFR exome
AF:
0.000517
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000364
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000366
Gnomad4 OTH exome
AF:
0.0000507
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000122
AC:
18
AN:
147430
Hom.:
0
Cov.:
0
AF XY:
0.000154
AC XY:
11
AN XY:
71516
show subpopulations
Gnomad4 AFR
AF:
0.000450
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
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.

Other links and lift over

dbSNP: rs10634555; hg19: chr3-42251577; API