rs13022357

Positions:

• chr2-159213245-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.3245-4252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,004 control chromosomes in the GnomAD database, including 52,786 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 0.83 (52786 hom., cov: 30)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC1	NM_033394.3	c.3245-4252A>G		intron_variant		ENST00000263635.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC1	ENST00000263635.8	c.3245-4252A>G		intron_variant		5	NM_033394.3	P1
TANC1	ENST00000470074.1	n.37-4252A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125955 AN: 151884 Hom.: 52754 Cov.: 30

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.829 AC: 126040 AN: 152004 Hom.: 52786 Cov.: 30 AF XY: 0.824 AC XY: 61174 AN XY: 74284

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.818

Alfa AF: 0.877 Hom.: 20731

Bravo AF: 0.829

Asia WGS AF: 0.712 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.31

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: rs13022357; hg19: chr2-160069756;