rs6550440

Positions:

• chr3-36897795-G-A
• chr3-36897795-G-T

Variant summary

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

The NM_001329998.2(TRANK1):​c.433+1314C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,062 control chromosomes in the GnomAD database, including 8,685 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 0.32 (8685 hom., cov: 33)
• Consequence: TRANK1 NM_001329998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRANK1	NM_001329998.2	c.433+1314C>T		intron_variant		ENST00000645898.2	NP_001316927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRANK1	ENST00000645898.2	c.433+1314C>T		intron_variant			NM_001329998.2	ENSP00000494480	P1
TRANK1	ENST00000429976.5	c.301+1314C>T		intron_variant		5		ENSP00000416168
TRANK1	ENST00000646897.1	c.409+1314C>T		intron_variant, NMD_transcript_variant				ENSP00000496771

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48794 AN: 151942 Hom.: 8670 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.321 AC: 48856 AN: 152062 Hom.: 8685 Cov.: 33 AF XY: 0.321 AC XY: 23850 AN XY: 74332

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.318

Alfa AF: 0.184 Hom.: 508

Bravo AF: 0.338

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.36

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: rs6550440; hg19: chr3-36939286;