Genetic Variant ENST00000496406.1:n.1987A>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 ENST00000496406.1(TANC1):n.1987A>G 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 0.0855 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
ENST00000496406.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.49

Publications

3 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:

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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	ENST00000496406.1 link	n.1987A>G	non_coding_transcript_exon_variant	Exon 1 of 2	1
TANC1	ENST00000263635.8 link	c.3903+600A>G	intron_variant	Intron 24 of 26	5	NM_033394.3	ENSP00000263635.6	Q9C0D5-1
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

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.0185

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.0781

AC:

AN:

European-Finnish (FIN)

AF:

0.0345

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0155

AC:

AN:

1480

Other (OTH)

AF:

0.0227

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

African (AFR)

AF:

0.216

AC:

8967

AN:

41470

American (AMR)

AF:

0.0366

AC:

560

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0374

AC:

130

AN:

3472

East Asian (EAS)

AF:

0.228

AC:

1178

AN:

5170

South Asian (SAS)

AF:

0.0721

AC:

348

AN:

4826

European-Finnish (FIN)

AF:

0.0643

AC:

683

AN:

10624

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0152

AC:

1035

AN:

68024

Other (OTH)

AF:

0.0691

AC:

146

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

566

1132

1699

2265

2831

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:

0.0634

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

(source)

DANN

Benign

0.34

PhyloP100

-3.5

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