rs11204846

chr1-151543604-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020127.3(TUFT1):c.60+3178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,002 control chromosomes in the GnomAD database, including 10,572 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 0.37 (10572 hom., cov: 31)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• 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+3178G>A		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.60+3178G>A		intron_variant		1	NM_020127.3	A1
	ENST00000434112.1	n.394+2695G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55750 AN: 151884 Hom.: 10567 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.367 AC: 55769 AN: 152002 Hom.: 10572 Cov.: 31 AF XY: 0.362 AC XY: 26880 AN XY: 74272

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.369

Alfa AF: 0.389 Hom.: 1445

Bravo AF: 0.362

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	17
Dann	Benign	0.84

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: rs11204846; hg19: chr1-151516080;