dbSNP rs2460111: TANC2:p.Gln289Gln (chr17-63237911-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001394998.1(TANC2):c.867G>A(p.Gln289Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 1,577,594 control chromosomes in the GnomAD database, including 216,744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.60 ( 29661 hom., cov: 31)

Exomes 𝑓: 0.51 ( 187083 hom. )

Consequence

TANC2
NM_001394998.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

TANC2 (HGNC:30212): (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2) Predicted to be involved in dense core granule cytoskeletal transport; regulation of dendritic spine development; and regulation of dendritic spine morphogenesis. Predicted to act upstream of or within in utero embryonic development. Located in dendritic spine. [provided by Alliance of Genome Resources, Apr 2022]

TANC2 links:

ENSG00000233635 (HGNC:):

ENSG00000233635 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 17-63237911-G-A is Benign according to our data. Variant chr17-63237911-G-A is described in ClinVar as [Benign]. Clinvar id is 3059740.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr17-63237911-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.4 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANC2	NM_001394998.1 link	c.867G>A	p.Gln289Gln	synonymous_variant	Exon 8 of 28	ENST00000689528.1	NP_001381927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC2	ENST00000689528.1 link	c.867G>A	p.Gln289Gln	synonymous_variant	Exon 8 of 28		NM_001394998.1	ENSP00000510600.1		A0A8I5KXR5

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

90738

AN:

151784

Hom.:

29601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.864

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.488

AC:

95380

AN:

195288

Hom.:

25232

AF XY:

0.487

AC XY:

50616

AN XY:

104036

show subpopulations

Gnomad AFR exome

AF:

0.875

Gnomad AMR exome

AF:

0.405

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.151

Gnomad SAS exome

AF:

0.483

Gnomad FIN exome

AF:

0.572

Gnomad NFE exome

AF:

0.508

Gnomad OTH exome

AF:

0.481

GnomAD4 exome

AF:

0.505

AC:

720526

AN:

1425692

Hom.:

187083

Cov.:

AF XY:

0.504

AC XY:

355404

AN XY:

705436

show subpopulations

Gnomad4 AFR exome

AF:

0.880

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.482

Gnomad4 EAS exome

AF:

0.220

Gnomad4 SAS exome

AF:

0.489

Gnomad4 FIN exome

AF:

0.563

Gnomad4 NFE exome

AF:

0.506

Gnomad4 OTH exome

AF:

0.509

GnomAD4 genome

AF:

0.598

AC:

90855

AN:

151902

Hom.:

29661

Cov.:

AF XY:

0.593

AC XY:

43989

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.864

Gnomad4 AMR

AF:

0.477

Gnomad4 ASJ

AF:

0.478

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.489

Gnomad4 FIN

AF:

0.570

Gnomad4 NFE

AF:

0.516

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.520

Hom.:

34552

Bravo

AF:

0.599

Asia WGS

AF:

0.409

AC:

1426

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TANC2-related disorder

Benign:1

Sep 24, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

3.6

DANN

Benign

0.75

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over