rs10490003

chr2-159226379-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.3903+600A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 153,980 control chromosomes in the GnomAD database, including 1,197 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 0.086 (1197 hom., cov: 33)
  • Exomes 𝑓: 0.020 (0 hom.)
• Consequence: TANC1 NM_033394.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

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=-0.91).
• 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/exons	MANE	UniProt
TANC1	NM_033394.3	c.3903+600A>G		intron_variant		ENST00000263635.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC1	ENST00000263635.8	c.3903+600A>G		intron_variant		5	NM_033394.3	P1
TANC1	ENST00000496406.1	n.1987A>G		non_coding_transcript_exon_variant	1/2	1
TANC1	ENST00000470074.1	n.1025+600A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0863 AC: 13121 AN: 152076 Hom.: 1195 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0679

GnomAD4 exome AF: 0.0202 AC: 36 AN: 1784 Hom.: 0 Cov.: 0 AF XY: 0.0250 AC XY: 23 AN XY: 920

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.0185

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.0781

Gnomad4 FIN exome AF: 0.0345

Gnomad4 NFE exome AF: 0.0155

Gnomad4 OTH exome AF: 0.0227

GnomAD4 genome AF: 0.0863 AC: 13132 AN: 152196 Hom.: 1197 Cov.: 33 AF XY: 0.0885 AC XY: 6584 AN XY: 74418

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.0152

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0578 Hom.: 96

Bravo AF: 0.0901

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.012
Dann	Benign	0.34

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: rs10490003; hg19: chr2-160082890;