rs7582141

chr2-159042977-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC1	NM_033394.3	c.-15-22919G>T		intron_variant		ENST00000263635.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC1	ENST00000263635.8	c.-15-22919G>T		intron_variant		5	NM_033394.3	P1

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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.0276

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0878 Hom.: 221

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	13
Dann	Benign	0.66

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: rs7582141; hg19: chr2-159899489;