NM_033394.3:c.3378+758C>G

Variant names:

• chr2-159218388-C-G
• rs10515928
• NM_033394.3:c.3378+758C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033394.3(TANC1):​c.3378+758C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,236 control chromosomes in the GnomAD database, including 1,202 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 0.087 (1202 hom., cov: 33)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANC1	NM_033394.3	c.3378+758C>G		intron_variant	Intron 20 of 26	ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8	c.3378+758C>G		intron_variant	Intron 20 of 26	5	NM_033394.3	ENSP00000263635.6
TANC1	ENST00000470074.1	n.170+758C>G		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13167 AN: 152118 Hom.: 1201 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0866 AC: 13177 AN: 152236 Hom.: 1202 Cov.: 33 AF XY: 0.0887 AC XY: 6601 AN XY: 74434

African (AFR) AF: 0.217 AC: 9017 AN: 41516

American (AMR) AF: 0.0365 AC: 558 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5164

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4828

European-Finnish (FIN) AF: 0.0639 AC: 678 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0152 AC: 1037 AN: 68024

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0554 Hom.: 77

Bravo AF: 0.0905

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.097
DANN	Benign	0.42
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10515928; hg19: chr2-160074899;