chr2-159097908-C-T

Variant names:

• chr2-159097908-C-T
• rs13414916
• NM_033394.3:c.259+74C>T

Variant summary

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

The NM_033394.3(TANC1):​c.259+74C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,242,178 control chromosomes in the GnomAD database, including 32,588 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 0.21 (3499 hom., cov: 32)
  • Exomes 𝑓: 0.22 (29089 hom.)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033394.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANC1	NM_033394.3	MANE Select	c.259+74C>T		intron	N/A	NP_203752.2	Q9C0D5-1
	TANC1	NM_001350064.2		c.259+74C>T		intron	N/A	NP_001336993.1
	TANC1	NM_001350065.2		c.259+74C>T		intron	N/A	NP_001336994.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANC1	ENST00000263635.8	TSL:5 MANE Select	c.259+74C>T		intron	N/A	ENSP00000263635.6	Q9C0D5-1
	TANC1	ENST00000851031.1		c.313+74C>T		intron	N/A	ENSP00000521100.1
	TANC1	ENST00000950898.1		c.313+74C>T		intron	N/A	ENSP00000620957.1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31799 AN: 151832 Hom.: 3490 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.223 AC: 243114 AN: 1090230 Hom.: 29089 AF XY: 0.226 AC XY: 124073 AN XY: 547886

African (AFR) AF: 0.171 AC: 4501 AN: 26262

American (AMR) AF: 0.212 AC: 8670 AN: 40868

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 3897 AN: 22798

East Asian (EAS) AF: 0.275 AC: 10183 AN: 37024

South Asian (SAS) AF: 0.349 AC: 24466 AN: 70180

European-Finnish (FIN) AF: 0.197 AC: 8053 AN: 40778

Middle Eastern (MID) AF: 0.189 AC: 752 AN: 3970

European-Non Finnish (NFE) AF: 0.215 AC: 172185 AN: 800772

Other (OTH) AF: 0.219 AC: 10407 AN: 47578

GnomAD4 genome AF: 0.210 AC: 31838 AN: 151948 Hom.: 3499 Cov.: 32 AF XY: 0.210 AC XY: 15563 AN XY: 74252

African (AFR) AF: 0.178 AC: 7370 AN: 41438

American (AMR) AF: 0.188 AC: 2863 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1550 AN: 5172

South Asian (SAS) AF: 0.362 AC: 1739 AN: 4800

European-Finnish (FIN) AF: 0.185 AC: 1944 AN: 10534

Middle Eastern (MID) AF: 0.142 AC: 41 AN: 288

European-Non Finnish (NFE) AF: 0.222 AC: 15066 AN: 67962

Other (OTH) AF: 0.198 AC: 418 AN: 2108

Alfa AF: 0.213 Hom.: 649

Bravo AF: 0.208

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-1.1
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: rs13414916; hg19: chr2-159954420; COSMIC: COSV55084681;