rs7211

Variant names:

• chr1-145993449-G-A
• rs7211
• NM_006472.6:c.*402C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-145993449-G-A
• chr1-145993449-G-C
• chr1-145993449-G-T

Variant summary

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

The NM_006472.6(TXNIP):​c.*402C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 164,592 control chromosomes in the GnomAD database, including 6,451 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 0.20 (6315 hom., cov: 32)
  • Exomes 𝑓: 0.11 (136 hom.)
• Consequence: TXNIP NM_006472.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 28 publications found

Genes affected

TXNIP (HGNC:16952): (thioredoxin interacting protein) This gene encodes a thioredoxin-binding protein that is a member of the alpha arrestin protein family. Thioredoxin is a thiol-oxidoreductase that is a major regulator of cellular redox signaling which protects cells from oxidative stress. This protein inhibits the antioxidative function of thioredoxin resulting in the accumulation of reactive oxygen species and cellular stress. This protein also functions as a regulator of cellular metabolism and of endoplasmic reticulum (ER) stress. This protein may also function as a tumor suppressor. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TXNIP	NM_006472.6	c.*402C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000582401.6	NP_006463.3
TXNIP	NM_001313972.2	c.*402C>T		3_prime_UTR_variant	Exon 7 of 7		NP_001300901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TXNIP	ENST00000582401.6	c.*402C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_006472.6	ENSP00000462521.1
TXNIP	ENST00000486597.1	n.*130C>T		downstream_gene_variant		2
TXNIP	ENST00000488537.1	n.*72C>T		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30277 AN: 151790 Hom.: 6281 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.106 AC: 1339 AN: 12684 Hom.: 136 Cov.: 0 AF XY: 0.108 AC XY: 736 AN XY: 6794

African (AFR) AF: 0.505 AC: 108 AN: 214

American (AMR) AF: 0.203 AC: 401 AN: 1980

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 25 AN: 324

East Asian (EAS) AF: 0.268 AC: 153 AN: 570

South Asian (SAS) AF: 0.131 AC: 245 AN: 1866

European-Finnish (FIN) AF: 0.0857 AC: 18 AN: 210

Middle Eastern (MID) AF: 0.125 AC: 5 AN: 40

European-Non Finnish (NFE) AF: 0.0445 AC: 306 AN: 6882

Other (OTH) AF: 0.130 AC: 78 AN: 598

GnomAD4 genome AF: 0.200 AC: 30372 AN: 151908 Hom.: 6315 Cov.: 32 AF XY: 0.200 AC XY: 14845 AN XY: 74254

African (AFR) AF: 0.521 AC: 21567 AN: 41386

American (AMR) AF: 0.192 AC: 2926 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.181 AC: 936 AN: 5162

South Asian (SAS) AF: 0.144 AC: 693 AN: 4814

European-Finnish (FIN) AF: 0.0662 AC: 698 AN: 10538

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2956 AN: 67976

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.0871 Hom.: 2069

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
PhyloP100		0.0070
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7211; hg19: chr1-145441620;