NM_001329998.2:c.5281-477T>A

Variant names:

• chr3-36839193-A-T
• rs4431050
• NM_001329998.2:c.5281-477T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001329998.2(TRANK1):​c.5281-477T>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: TRANK1 NM_001329998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 3 publications found

Genes affected

TRANK1 (HGNC:29011): (tetratricopeptide repeat and ankyrin repeat containing 1) Predicted to enable ATP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329998.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRANK1	NM_001329998.2	MANE Select	c.5281-477T>A		intron	N/A	NP_001316927.1
	TRANK1	NM_014831.3		c.5149-477T>A		intron	N/A	NP_055646.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRANK1	ENST00000645898.2	MANE Select	c.5281-477T>A		intron	N/A	ENSP00000494480.1
	TRANK1	ENST00000429976.6	TSL:5	c.5149-477T>A		intron	N/A	ENSP00000416168.2
	TRANK1	ENST00000643881.1		n.*1631-477T>A		intron	N/A	ENSP00000496256.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.51
PhyloP100		0.48

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

Other links and lift over

dbSNP: rs4431050; hg19: chr3-36880684;