rs7582141

Variant names:

• chr2-159042977-G-T
• rs7582141
• NM_033394.3:c.-15-22919G>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.-15-22919G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,100 control chromosomes in the GnomAD database, including 1,930 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 (1930 hom., cov: 31)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 18 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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.-15-22919G>T		intron	N/A	NP_203752.2	Q9C0D5-1
	TANC1	NM_001350064.2		c.-15-22919G>T		intron	N/A	NP_001336993.1
	TANC1	NM_001350065.2		c.-184-299G>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.-15-22919G>T		intron	N/A	ENSP00000263635.6	Q9C0D5-1
	TANC1	ENST00000851031.1		c.-15-22919G>T		intron	N/A	ENSP00000521100.1
	TANC1	ENST00000950898.1		c.-15-22919G>T		intron	N/A	ENSP00000620957.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18041 AN: 151982 Hom.: 1928 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0276

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.119 AC: 18066 AN: 152100 Hom.: 1930 Cov.: 31 AF XY: 0.122 AC XY: 9076 AN XY: 74366

African (AFR) AF: 0.276 AC: 11429 AN: 41454

American (AMR) AF: 0.160 AC: 2449 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.162 AC: 833 AN: 5154

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4824

European-Finnish (FIN) AF: 0.0715 AC: 758 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0276 AC: 1880 AN: 68000

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0625 Hom.: 1139

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		0.91
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: rs7582141; hg19: chr2-159899489;