rs7554707

chr1-151569239-G-T

Variant summary

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

The NM_020127.3(TUFT1):c.481-418G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,974 control chromosomes in the GnomAD database, including 25,742 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 0.56 (25742 hom., cov: 31)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUFT1	NM_020127.3	c.481-418G>T		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.481-418G>T		intron_variant		1	NM_020127.3	A1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85458 AN: 151856 Hom.: 25751 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.562 AC: 85478 AN: 151974 Hom.: 25742 Cov.: 31 AF XY: 0.556 AC XY: 41279 AN XY: 74264

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.605

Alfa AF: 0.664 Hom.: 45895

Bravo AF: 0.551

Asia WGS AF: 0.456 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.4
Dann	Benign	0.61

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: rs7554707; hg19: chr1-151541715;