Variant 3-36896030-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001329998.2(TRANK1):c.434-272C>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 151,978 control chromosomes in the GnomAD database, including 8,674 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 ( 8674 hom., cov: 32)

Consequence

TRANK1
NM_001329998.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.97

Variant links:

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]

TRANK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRANK1	NM_001329998.2 linkuse as main transcript	c.434-272C>T		intron_variant		ENST00000645898.2	NP_001316927.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
TRANK1	ENST00000645898.2 linkuse as main transcript	c.434-272C>T	intron_variant		NM_001329998.2	ENSP00000494480	P1
TRANK1	ENST00000429976.5 linkuse as main transcript	c.302-272C>T	intron_variant	5		ENSP00000416168
TRANK1	ENST00000646897.1 linkuse as main transcript	c.410-272C>T	intron_variant, NMD_transcript_variant			ENSP00000496771

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48736

AN:

151860

Hom.:

8660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.321

AC:

48796

AN:

151978

Hom.:

8674

Cov.:

AF XY:

0.321

AC XY:

23811

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.335

Gnomad4 ASJ

AF:

0.286

Gnomad4 EAS

AF:

0.566

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.280

Hom.:

782

Bravo

AF:

0.338

Asia WGS

AF:

0.438

AC:

1523

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.3

DANN

Benign

0.33

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over