dbSNP rs10490005: TANC1:c.3379-104A>C (chr2-159219134-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033394.3(TANC1):c.3379-104A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 1,466,976 control chromosomes in the GnomAD database, including 3,614 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 0.087 ( 1210 hom., cov: 33)

Exomes 𝑓: 0.032 ( 2404 hom. )

Consequence

TANC1
NM_033394.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.528

Publications

4 publications found

Variant links:

Genes affected

TANC1 (HGNC:29364): (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1) Predicted to be involved in regulation of postsynapse organization. Predicted to act upstream of or within dendritic spine maintenance; myoblast fusion; and visual learning. Predicted to be located in several cellular components, including axon terminus; neuronal cell body; and postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component. [provided by Alliance of Genome Resources, Apr 2022]

TANC1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANC1	NM_033394.3 link	c.3379-104A>C		intron_variant	Intron 20 of 26	ENST00000263635.8	NP_203752.2	Q9C0D5-1B9EK39

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8 link	c.3379-104A>C		intron_variant	Intron 20 of 26	5	NM_033394.3	ENSP00000263635.6		Q9C0D5-1
TANC1	ENST00000470074.1 link	n.171-104A>C		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.0867

AC:

13190

AN:

152200

Hom.:

1209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.0375

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.0735

Gnomad FIN

AF:

0.0643

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0153

Gnomad OTH

AF:

0.0678

GnomAD4 exome

AF:

0.0324

AC:

42548

AN:

1314658

Hom.:

2404

AF XY:

0.0329

AC XY:

21593

AN XY:

656930

show subpopulations

African (AFR)

AF:

0.217

AC:

6519

AN:

30048

American (AMR)

AF:

0.0225

AC:

969

AN:

43002

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

960

AN:

24332

East Asian (EAS)

AF:

0.241

AC:

9277

AN:

38504

South Asian (SAS)

AF:

0.0656

AC:

5320

AN:

81068

European-Finnish (FIN)

AF:

0.0538

AC:

2829

AN:

52572

Middle Eastern (MID)

AF:

0.0314

AC:

138

AN:

4392

European-Non Finnish (NFE)

AF:

0.0145

AC:

14283

AN:

985706

Other (OTH)

AF:

0.0409

AC:

2253

AN:

55034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1849

3699

5548

7398

9247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

772

1544

2316

3088

3860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0867

AC:

13200

AN:

152318

Hom.:

1210

Cov.:

AF XY:

0.0889

AC XY:

6621

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.217

AC:

9025

AN:

41548

American (AMR)

AF:

0.0364

AC:

558

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0375

AC:

130

AN:

3470

East Asian (EAS)

AF:

0.228

AC:

1183

AN:

5188

South Asian (SAS)

AF:

0.0727

AC:

351

AN:

4828

European-Finnish (FIN)

AF:

0.0643

AC:

683

AN:

10620

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0153

AC:

1039

AN:

68030

Other (OTH)

AF:

0.0690

AC:

146

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

551

1102

1654

2205

2756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0637

Hom.:

108

Bravo

AF:

0.0905

Asia WGS

AF:

0.166

AC:

576

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.5

(source)

DANN

Benign

0.52

PhyloP100

0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over