rs264651

Positions:

• chr2-159072919-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANC1	NM_033394.3	c.61+6948A>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.61+6948A>G		intron_variant		5	NM_033394.3	ENSP00000263635	P1

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0270

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0655 Hom.: 91

Bravo AF: 0.0753

Asia WGS AF: 0.132 AC: 458 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	0.17
DANN	Benign	0.72

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: rs264651; hg19: chr2-159929431;