rs890049

Variant names:

• chr2-217880163-C-T
• rs890049
• NM_001387777.1:c.1429+735G>A

Variant summary

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

The NM_001387777.1(TNS1):​c.1429+735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,052 control chromosomes in the GnomAD database, including 12,500 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 0.40 (12500 hom., cov: 32)
• Consequence: TNS1 NM_001387777.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 5 publications found

Genes affected

TNS1 (HGNC:11973): (tensin 1) The protein encoded by this gene localizes to focal adhesions, regions of the plasma membrane where the cell attaches to the extracellular matrix. This protein crosslinks actin filaments and contains a Src homology 2 (SH2) domain, which is often found in molecules involved in signal transduction. This protein is a substrate of calpain II. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNS1	NM_001387777.1	c.1429+735G>A		intron_variant	Intron 18 of 32	ENST00000682258.1	NP_001374706.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNS1	ENST00000682258.1	c.1429+735G>A		intron_variant	Intron 18 of 32		NM_001387777.1	ENSP00000506917.1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60831 AN: 151932 Hom.: 12488 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.400 AC: 60889 AN: 152052 Hom.: 12500 Cov.: 32 AF XY: 0.396 AC XY: 29428 AN XY: 74324

African (AFR) AF: 0.363 AC: 15044 AN: 41464

American (AMR) AF: 0.358 AC: 5474 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1292 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1591 AN: 5174

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4810

European-Finnish (FIN) AF: 0.434 AC: 4584 AN: 10572

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30043 AN: 67978

Other (OTH) AF: 0.379 AC: 796 AN: 2100

Alfa AF: 0.418 Hom.: 30132

Bravo AF: 0.390

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.64
PhyloP100		-0.067
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: rs890049; hg19: chr2-218744886;