dbSNP rs2241023: TANC1:n.433G>C (chr2-159224825-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000496406.1(TANC1):n.433G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 163,718 control chromosomes in the GnomAD database, including 1,234 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 0.086 ( 1198 hom., cov: 32)

Exomes 𝑓: 0.042 ( 36 hom. )

Consequence

TANC1
ENST00000496406.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.769

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=-0.86).

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.3811+461G>C		intron_variant	Intron 23 of 26	ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
TANC1	ENST00000496406.1 link	n.433G>C	non_coding_transcript_exon_variant	Exon 1 of 2	1
TANC1	ENST00000263635.8 link	c.3811+461G>C	intron_variant	Intron 23 of 26	5	NM_033394.3	ENSP00000263635.6
TANC1	ENST00000470074.1 link	n.933+461G>C	intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.0863

AC:

13129

AN:

152084

Hom.:

1197

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:

0.0720

Gnomad FIN

AF:

0.0642

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0674

GnomAD4 exome

AF:

0.0418

AC:

481

AN:

11516

Hom.:

Cov.:

AF XY:

0.0430

AC XY:

258

AN XY:

6004

show subpopulations

African (AFR)

AF:

0.171

AC:

AN:

572

American (AMR)

AF:

0.0183

AC:

AN:

2130

Ashkenazi Jewish (ASJ)

AF:

0.0543

AC:

AN:

184

East Asian (EAS)

AF:

0.209

AC:

173

AN:

828

South Asian (SAS)

AF:

0.0630

AC:

AN:

968

European-Finnish (FIN)

AF:

0.0203

AC:

AN:

148

Middle Eastern (MID)

AF:

0.0417

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0133

AC:

AN:

6170

Other (OTH)

AF:

0.0285

AC:

AN:

492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0863

AC:

13138

AN:

152202

Hom.:

1198

Cov.:

AF XY:

0.0885

AC XY:

6581

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.216

AC:

8984

AN:

41510

American (AMR)

AF:

0.0364

AC:

557

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0375

AC:

130

AN:

3470

East Asian (EAS)

AF:

0.228

AC:

1176

AN:

5162

South Asian (SAS)

AF:

0.0713

AC:

343

AN:

4814

European-Finnish (FIN)

AF:

0.0642

AC:

681

AN:

10612

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0152

AC:

1037

AN:

68016

Other (OTH)

AF:

0.0686

AC:

145

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

539

1078

1616

2155

2694

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:

0.0189

Hom.:

Bravo

AF:

0.0903

Asia WGS

AF:

0.166

AC:

578

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.81

(source)

DANN

Benign

0.51

PhyloP100

-0.77

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