rs1498095

Variant names:

• chr3-42051930-T-A
• ENST00000673621.2:c.-122-35174T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-42051930-T-A
• chr3-42051930-T-C
• chr3-42051930-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000673621.2(TRAK1):​c.-122-35174T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TRAK1 ENST00000673621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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]

RPL7AP83 (HGNC:56412): (ribosomal protein L7a pseudogene 83)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAK1	XM_017005909.2	c.-518-35174T>A		intron_variant	Intron 1 of 16		XP_016861398.1
TRAK1	XM_047447718.1	c.-518-35174T>A		intron_variant	Intron 1 of 16		XP_047303674.1
TRAK1	XM_047447722.1	c.-518-35174T>A		intron_variant	Intron 1 of 16		XP_047303678.1
TRAK1	XM_017005911.2	c.-518-35174T>A		intron_variant	Intron 1 of 16		XP_016861400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAK1	ENST00000673621.2	c.-122-35174T>A		intron_variant	Intron 1 of 16			ENSP00000500819.2
TRAK1	ENST00000487159.5	c.-518-35174T>A		intron_variant	Intron 1 of 16	5		ENSP00000486713.1
TRAK1	ENST00000672026.1	c.-518-35174T>A		intron_variant	Intron 1 of 17			ENSP00000500099.1
RPL7AP83	ENST00000434712.1	n.-236A>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-42093422;