Variant rs3828054 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020127.3(TUFT1):c.53A>G(p.Gln18Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,613,936 control chromosomes in the GnomAD database, including 12,030 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1256 hom., cov: 33)

Exomes 𝑓: 0.12 ( 10774 hom. )

Consequence

TUFT1
NM_020127.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.69

Variant links:

Genes affected

TUFT1 (HGNC:12422): (tuftelin 1) Tuftelin is an acidic protein that is thought to play a role in dental enamel mineralization and is implicated in caries susceptibility. It is also thought to be involved with adaptation to hypoxia, mesenchymal stem cell function, and neurotrophin nerve growth factor mediated neuronal differentiation. [provided by RefSeq, Aug 2014]

TUFT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0011017025).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUFT1	NM_020127.3 linkuse as main transcript	c.53A>G	p.Gln18Arg	missense_variant	1/13	ENST00000368849.8	NP_064512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUFT1	ENST00000368849.8 linkuse as main transcript	c.53A>G	p.Gln18Arg	missense_variant	1/13	1	NM_020127.3	ENSP00000357842	A1	Q9NNX1-1
TUFT1	ENST00000368848.6 linkuse as main transcript	c.53A>G	p.Gln18Arg	missense_variant	1/12	1		ENSP00000357841	P4	Q9NNX1-2
TUFT1	ENST00000392712.7 linkuse as main transcript	c.53A>G	p.Gln18Arg	missense_variant	1/11	5		ENSP00000376476
TUFT1	ENST00000498606.5 linkuse as main transcript	n.86A>G		non_coding_transcript_exon_variant	1/7	2

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19414

AN:

152172

Hom.:

1258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.0863

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.0557

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.114

AC:

28561

AN:

250812

Hom.:

1790

AF XY:

0.113

AC XY:

15313

AN XY:

135648

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.0699

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.0522

Gnomad SAS exome

AF:

0.0985

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.119

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.118

AC:

172978

AN:

1461646

Hom.:

10774

Cov.:

AF XY:

0.117

AC XY:

85415

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.145

Gnomad4 AMR exome

AF:

0.0727

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.0557

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.127

AC:

19415

AN:

152290

Hom.:

1256

Cov.:

AF XY:

0.130

AC XY:

9709

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.0863

Gnomad4 ASJ

AF:

0.113

Gnomad4 EAS

AF:

0.0558

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.119

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.115

Hom.:

2534

Bravo

AF:

0.122

TwinsUK

AF:

0.115

AC:

425

ALSPAC

AF:

0.119

AC:

458

ESP6500AA

AF:

0.154

AC:

678

ESP6500EA

AF:

0.124

AC:

1069

ExAC

AF:

0.116

AC:

14059

Asia WGS

AF:

0.106

AC:

369

AN:

3478

EpiCase

AF:

0.110

EpiControl

AF:

0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.031

T;T;.;T

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.43

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.43

T;T;T;T

MetaRNN

Benign

0.0011

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.3

M;.;M;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.080

N;N;N;N

REVEL

Benign

0.068

Sift

Benign

0.49

T;T;D;T

Sift4G

Benign

0.38

T;T;T;T

Polyphen

0.69

P;.;P;.

Vest4

0.23

MPC

0.21

ClinPred

0.012

GERP RS

2.5

Varity_R

0.053

gMVP

0.15

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over