dbSNP rs10490003: TANC1:c.3903+600A>G (chr2-159226379-A-G) – 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.3903+600A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 153,980 control chromosomes in the GnomAD database, including 1,197 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 ( 1197 hom., cov: 33)

Exomes 𝑓: 0.020 ( 0 hom. )

Consequence

TANC1
NM_033394.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.49

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:

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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=-0.91).

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.3903+600A>G		intron_variant	Intron 24 of 26	ENST00000263635.8	NP_203752.2	Q9C0D5-1B9EK39

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TANC1	ENST00000263635.8 link	c.3903+600A>G	intron_variant	Intron 24 of 26	5	NM_033394.3	ENSP00000263635.6	Q9C0D5-1
TANC1	ENST00000496406.1 link	n.1987A>G	non_coding_transcript_exon_variant	Exon 1 of 2	1
TANC1	ENST00000470074.1 link	n.1025+600A>G	intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.0863

AC:

13121

AN:

152076

Hom.:

1195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0367

Gnomad ASJ

AF:

0.0374

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.0729

Gnomad FIN

AF:

0.0643

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0679

GnomAD4 exome

AF:

0.0202

AC:

AN:

1784

Hom.:

Cov.:

AF XY:

0.0250

AC XY:

AN XY:

920

show subpopulations

Gnomad4 AFR exome

AF:

0.167

AC:

AN:

Gnomad4 AMR exome

AF:

0.0185

AC:

AN:

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

Gnomad4 EAS exome

AF:

0.125

AC:

AN:

Gnomad4 SAS exome

AF:

0.0781

AC:

AN:

Gnomad4 FIN exome

AF:

0.0345

AC:

AN:

Gnomad4 NFE exome

AF:

0.0155

AC:

AN:

1480

Gnomad4 Remaining exome

AF:

0.0227

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<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:

13132

AN:

152196

Hom.:

1197

Cov.:

AF XY:

0.0885

AC XY:

6584

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.216

AC:

0.216229

AN:

0.216229

Gnomad4 AMR

AF:

0.0366

AC:

0.0366205

AN:

0.0366205

Gnomad4 ASJ

AF:

0.0374

AC:

0.0374424

AN:

0.0374424

Gnomad4 EAS

AF:

0.228

AC:

0.227853

AN:

0.227853

Gnomad4 SAS

AF:

0.0721

AC:

0.0721094

AN:

0.0721094

Gnomad4 FIN

AF:

0.0643

AC:

0.0642884

AN:

0.0642884

Gnomad4 NFE

AF:

0.0152

AC:

0.0152152

AN:

0.0152152

Gnomad4 OTH

AF:

0.0691

AC:

0.0691288

AN:

0.0691288

Heterozygous variant carriers

566

1132

1699

2265

2831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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:

0.0634

Hom.:

114

Bravo

AF:

0.0901

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

-0.91

CADD

Benign

0.012

DANN

Benign

0.34

Mutation Taster

=100/0

polymorphism (auto)

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