2-159094353-C-G

Position:

• chr2-159094353-C-G

Variant summary

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

The NM_033394.3(TANC1):​c.62-3284C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,178 control chromosomes in the GnomAD database, including 2,806 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 0.14 (2806 hom., cov: 32)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANC1	NM_033394.3	c.62-3284C>G		intron_variant		ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8	c.62-3284C>G		intron_variant		5	NM_033394.3	ENSP00000263635	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21355 AN: 152060 Hom.: 2797 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.141 AC: 21400 AN: 152178 Hom.: 2806 Cov.: 32 AF XY: 0.145 AC XY: 10802 AN XY: 74392

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0934 Hom.: 231

Bravo AF: 0.156

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.63

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: rs264631; hg19: chr2-159950865;