1-151552082-T-C

Variant summary

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

The NM_020127.3(TUFT1):c.61-10009T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,060 control chromosomes in the GnomAD database, including 24,542 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 0.55 (24542 hom., cov: 31)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUFT1	NM_020127.3	c.61-10009T>C		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.61-10009T>C		intron_variant		1	NM_020127.3	A1
	ENST00000434112.1	n.395-9642T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84144 AN: 151938 Hom.: 24518 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.554 AC: 84198 AN: 152060 Hom.: 24542 Cov.: 31 AF XY: 0.562 AC XY: 41780 AN XY: 74328

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.570

Alfa AF: 0.572 Hom.: 5135

Bravo AF: 0.549

Asia WGS AF: 0.693 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.3
Dann	Benign	0.80

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: rs7526319; hg19: chr1-151524558;