rs264588

Variant names:

• chr2-159079879-C-A
• rs264588
• NM_033394.3:c.61+13908C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-159079879-C-A
• chr2-159079879-C-G
• chr2-159079879-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-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 rank	MANE	Protein	UniProt
TANC1	NM_033394.3	c.61+13908C>A		intron_variant	Intron 3 of 26	ENST00000263635.8	NP_203752.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC1	ENST00000263635.8	c.61+13908C>A		intron_variant	Intron 3 of 26	5	NM_033394.3	ENSP00000263635.6

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

African (AFR) AF: 0.286 AC: 11869 AN: 41476

American (AMR) AF: 0.162 AC: 2471 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3468

East Asian (EAS) AF: 0.147 AC: 764 AN: 5182

South Asian (SAS) AF: 0.114 AC: 548 AN: 4818

European-Finnish (FIN) AF: 0.0731 AC: 775 AN: 10604

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0281 AC: 1908 AN: 68020

Other (OTH) AF: 0.110 AC: 233 AN: 2112

Alfa AF: 0.0567 Hom.: 1080

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
PhyloP100		-0.27
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: rs264588; hg19: chr2-159936391;