rs9872588

Positions:

• chr3-42142681-T-G

Variant summary

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

The NM_001042646.3(TRAK1):​c.286+17067T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,314 control chromosomes in the GnomAD database, including 516 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 0.074 (516 hom., cov: 33)
• Consequence: TRAK1 NM_001042646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAK1	NM_001042646.3	c.286+17067T>G		intron_variant		ENST00000327628.10	NP_001036111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAK1	ENST00000327628.10	c.286+17067T>G		intron_variant		1	NM_001042646.3	ENSP00000328998.5

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11293 AN: 152196 Hom.: 516 Cov.: 33

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0741 AC: 11293 AN: 152314 Hom.: 516 Cov.: 33 AF XY: 0.0731 AC XY: 5448 AN XY: 74480

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0950 Hom.: 764

Bravo AF: 0.0678

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.85

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: rs9872588; hg19: chr3-42184173;