rs3821301

Positions:

• chr2-159231024-T-G

Variant summary

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

The NM_033394.3(TANC1):​c.*12T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 1,560,238 control chromosomes in the GnomAD database, including 591,980 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 0.82 (51371 hom., cov: 32)
  • Exomes 𝑓: 0.87 (540609 hom.)
• Consequence: TANC1 NM_033394.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANC1	NM_033394.3	c.*12T>G		3_prime_UTR_variant	27/27	ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8	c.*12T>G		3_prime_UTR_variant	27/27	5	NM_033394.3	ENSP00000263635	P1
TANC1	ENST00000496406.1	n.5951T>G		non_coding_transcript_exon_variant	2/2	1
TANC1	ENST00000470074.1	n.2720T>G		non_coding_transcript_exon_variant	8/8	5

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124074 AN: 152048 Hom.: 51344 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.813

GnomAD3 exomes AF: 0.838 AC: 185308 AN: 221136 Hom.: 78415 AF XY: 0.836 AC XY: 100679 AN XY: 120414

Gnomad AFR exome AF: 0.689

Gnomad AMR exome AF: 0.925

Gnomad ASJ exome AF: 0.808

Gnomad EAS exome AF: 0.660

Gnomad SAS exome AF: 0.747

Gnomad FIN exome AF: 0.823

Gnomad NFE exome AF: 0.890

Gnomad OTH exome AF: 0.862

GnomAD4 exome AF: 0.874 AC: 1230256 AN: 1408072 Hom.: 540609 Cov.: 27 AF XY: 0.869 AC XY: 604145 AN XY: 694870

Gnomad4 AFR exome AF: 0.674

Gnomad4 AMR exome AF: 0.919

Gnomad4 ASJ exome AF: 0.801

Gnomad4 EAS exome AF: 0.674

Gnomad4 SAS exome AF: 0.747

Gnomad4 FIN exome AF: 0.829

Gnomad4 NFE exome AF: 0.900

Gnomad4 OTH exome AF: 0.847

GnomAD4 genome AF: 0.816 AC: 124151 AN: 152166 Hom.: 51371 Cov.: 32 AF XY: 0.810 AC XY: 60233 AN XY: 74388

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.813

Alfa AF: 0.873 Hom.: 120707

Bravo AF: 0.816

Asia WGS AF: 0.710 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.43

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: rs3821301; hg19: chr2-160087535; COSMIC: COSV55085035; COSMIC: COSV55085035;