rs2337360

chr1-151542127-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.60+1701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,040 control chromosomes in the GnomAD database, including 9,433 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 0.34 (9433 hom., cov: 32)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUFT1	NM_020127.3	c.60+1701G>A		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.60+1701G>A		intron_variant		1	NM_020127.3	A1
	ENST00000434112.1	n.394+1218G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52218 AN: 151920 Hom.: 9430 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.344 AC: 52235 AN: 152040 Hom.: 9433 Cov.: 32 AF XY: 0.339 AC XY: 25196 AN XY: 74316

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.357

Alfa AF: 0.400 Hom.: 22686

Bravo AF: 0.336

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
Dann	Benign	0.71

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: rs2337360; hg19: chr1-151514603;