rs3790506

Positions:

• chr1-151565890-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020127.3(TUFT1):​c.415-273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 328,736 control chromosomes in the GnomAD database, including 13,260 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 0.26 (5576 hom., cov: 32)
  • Exomes 𝑓: 0.28 (7684 hom.)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUFT1	NM_020127.3	c.415-273G>A		intron_variant		ENST00000368849.8	NP_064512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUFT1	ENST00000368849.8	c.415-273G>A		intron_variant		1	NM_020127.3	ENSP00000357842	A1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38825 AN: 151794 Hom.: 5579 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.285 AC: 50318 AN: 176824 Hom.: 7684 Cov.: 0 AF XY: 0.286 AC XY: 26939 AN XY: 94048

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.213

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.320

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.270

GnomAD4 genome AF: 0.256 AC: 38829 AN: 151912 Hom.: 5576 Cov.: 32 AF XY: 0.255 AC XY: 18966 AN XY: 74238

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.271

Alfa AF: 0.298 Hom.: 8369

Bravo AF: 0.258

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.039
DANN	Benign	0.55

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: rs3790506; hg19: chr1-151538366;