rs264588

chr2-159079879-C-Achr2-159079879-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033394.3(TANC1):c.61+13908C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,186 control chromosomes in the GnomAD database, including 2,072 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 (2072 hom., cov: 32)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC1	NM_033394.3	c.61+13908C>A		intron_variant		ENST00000263635.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC1	ENST00000263635.8	c.61+13908C>A		intron_variant		5	NM_033394.3	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18876 AN: 152068 Hom.: 2067 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.124 AC: 18908 AN: 152186 Hom.: 2072 Cov.: 32 AF XY: 0.129 AC XY: 9581 AN XY: 74408

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0509 Hom.: 229

Bravo AF: 0.137

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.0
Dann	Benign	0.58

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: rs264588; hg19: chr2-159936391;