3-36839193-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001329998.2(TRANK1):​c.5281-477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,176 control chromosomes in the GnomAD database, including 55,373 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 0.85 (55373 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

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>C		intron	N/A	NP_001316927.1
	TRANK1	NM_014831.3		c.5149-477T>C		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>C		intron	N/A	ENSP00000494480.1
	TRANK1	ENST00000429976.6	TSL:5	c.5149-477T>C		intron	N/A	ENSP00000416168.2
	TRANK1	ENST00000643881.1		n.*1631-477T>C		intron	N/A	ENSP00000496256.1

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128791 AN: 152058 Hom.: 55359 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.847 AC: 128850 AN: 152176 Hom.: 55373 Cov.: 32 AF XY: 0.848 AC XY: 63123 AN XY: 74420

African (AFR) AF: 0.701 AC: 29074 AN: 41478

American (AMR) AF: 0.808 AC: 12350 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3301 AN: 3470

East Asian (EAS) AF: 0.958 AC: 4957 AN: 5172

South Asian (SAS) AF: 0.865 AC: 4173 AN: 4822

European-Finnish (FIN) AF: 0.957 AC: 10167 AN: 10620

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61899 AN: 68006

Other (OTH) AF: 0.869 AC: 1833 AN: 2110

Alfa AF: 0.890 Hom.: 142201

Bravo AF: 0.828

Asia WGS AF: 0.890 AC: 3097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.47
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

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;