2-159072919-A-G

Variant names:

• chr2-159072919-A-G
• rs264651
• NM_033394.3:c.61+6948A>G

Variant summary

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

The NM_033394.3(TANC1):​c.61+6948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 152,310 control chromosomes in the GnomAD database, including 559 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 0.070 (559 hom., cov: 33)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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.61+6948A>G		intron	N/A	NP_203752.2	Q9C0D5-1
	TANC1	NM_001350064.2		c.61+6948A>G		intron	N/A	NP_001336993.1
	TANC1	NM_001350065.2		c.61+6948A>G		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.61+6948A>G		intron	N/A	ENSP00000263635.6	Q9C0D5-1
	TANC1	ENST00000851031.1		c.62-3556A>G		intron	N/A	ENSP00000521100.1
	TANC1	ENST00000950898.1		c.62-3556A>G		intron	N/A	ENSP00000620957.1

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10690 AN: 152194 Hom.: 556 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0655

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

GnomAD4 genome AF: 0.0703 AC: 10704 AN: 152310 Hom.: 559 Cov.: 33 AF XY: 0.0762 AC XY: 5677 AN XY: 74460

African (AFR) AF: 0.103 AC: 4270 AN: 41560

American (AMR) AF: 0.139 AC: 2128 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.148 AC: 767 AN: 5188

South Asian (SAS) AF: 0.107 AC: 517 AN: 4824

European-Finnish (FIN) AF: 0.0730 AC: 775 AN: 10618

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0270 AC: 1835 AN: 68032

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0487 Hom.: 457

Bravo AF: 0.0753

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-0.40
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: rs264651; hg19: chr2-159929431;