chr2-159043401-C-T

Variant names:

• chr2-159043401-C-T
• rs6432512
• NM_033394.3:c.-15-22495C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350065.2(TANC1):​c.-59C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,950 control chromosomes in the GnomAD database, including 2,031 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 0.12 (2031 hom., cov: 31)
• Consequence: TANC1 NM_001350065.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANC1	NM_033394.3	c.-15-22495C>T		intron_variant	Intron 2 of 26	ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8	c.-15-22495C>T		intron_variant	Intron 2 of 26	5	NM_033394.3	ENSP00000263635.6

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18432 AN: 151832 Hom.: 2029 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.121 AC: 18459 AN: 151950 Hom.: 2031 Cov.: 31 AF XY: 0.125 AC XY: 9267 AN XY: 74296

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0810 Hom.: 156

Bravo AF: 0.137

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.074
DANN	Benign	0.37

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

Other links and lift over

dbSNP: rs6432512; hg19: chr2-159899913;