ENST00000496406.1:n.5951T>G

Variant names:

• chr2-159231024-T-G
• rs3821301
• ENST00000496406.1:n.5951T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000496406.1(TANC1):​n.5951T>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 0.868 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 ENST00000496406.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 26 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000496406.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANC1	NM_033394.3	MANE Select	c.*12T>G		3_prime_UTR	Exon 27 of 27	NP_203752.2
	TANC1	NM_001350064.2		c.*12T>G		3_prime_UTR	Exon 27 of 27	NP_001336993.1
	TANC1	NM_001350065.2		c.*12T>G		3_prime_UTR	Exon 28 of 28	NP_001336994.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANC1	ENST00000496406.1	TSL:1	n.5951T>G		non_coding_transcript_exon	Exon 2 of 2
	TANC1	ENST00000263635.8	TSL:5 MANE Select	c.*12T>G		3_prime_UTR	Exon 27 of 27	ENSP00000263635.6
	TANC1	ENST00000470074.1	TSL:5	n.2720T>G		non_coding_transcript_exon	Exon 8 of 8

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

GnomAD2 exomes AF: 0.838 AC: 185308 AN: 221136 AF XY: 0.836

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 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

African (AFR) AF: 0.674 AC: 21063 AN: 31254

American (AMR) AF: 0.919 AC: 33380 AN: 36306

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 19148 AN: 23918

East Asian (EAS) AF: 0.674 AC: 26281 AN: 38970

South Asian (SAS) AF: 0.747 AC: 59397 AN: 79478

European-Finnish (FIN) AF: 0.829 AC: 42887 AN: 51708

Middle Eastern (MID) AF: 0.813 AC: 4506 AN: 5542

European-Non Finnish (NFE) AF: 0.900 AC: 974524 AN: 1082968

Other (OTH) AF: 0.847 AC: 49070 AN: 57928

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

African (AFR) AF: 0.690 AC: 28626 AN: 41494

American (AMR) AF: 0.886 AC: 13554 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2810 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3446 AN: 5180

South Asian (SAS) AF: 0.728 AC: 3504 AN: 4810

European-Finnish (FIN) AF: 0.816 AC: 8636 AN: 10578

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.894 AC: 60809 AN: 68020

Other (OTH) AF: 0.813 AC: 1720 AN: 2116

Alfa AF: 0.863 Hom.: 180906

Bravo AF: 0.816

Asia WGS AF: 0.710 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.43
PhyloP100		0.17
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

Other links and lift over

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