rs3748608

chr1-151578844-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.924+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 1,544,108 control chromosomes in the GnomAD database, including 335,994 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 (26072 hom., cov: 32)
  • Exomes 𝑓: 0.66 (309922 hom.)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUFT1	NM_020127.3	c.924+18G>A		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.924+18G>A		intron_variant		1	NM_020127.3	A1
TUFT1	ENST00000368848.6	c.849+18G>A		intron_variant		1		P4
TUFT1	ENST00000392712.7	c.759+18G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85474 AN: 152014 Hom.: 26074 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.610

GnomAD3 exomes AF: 0.592 AC: 95960 AN: 162144 Hom.: 29675 AF XY: 0.597 AC XY: 51058 AN XY: 85560

Gnomad AFR exome AF: 0.316

Gnomad AMR exome AF: 0.530

Gnomad ASJ exome AF: 0.718

Gnomad EAS exome AF: 0.369

Gnomad SAS exome AF: 0.542

Gnomad FIN exome AF: 0.570

Gnomad NFE exome AF: 0.700

Gnomad OTH exome AF: 0.656

GnomAD4 exome AF: 0.662 AC: 920946 AN: 1391976 Hom.: 309922 Cov.: 30 AF XY: 0.659 AC XY: 452976 AN XY: 686960

Gnomad4 AFR exome AF: 0.319

Gnomad4 AMR exome AF: 0.541

Gnomad4 ASJ exome AF: 0.717

Gnomad4 EAS exome AF: 0.424

Gnomad4 SAS exome AF: 0.540

Gnomad4 FIN exome AF: 0.574

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 0.641

GnomAD4 genome AF: 0.562 AC: 85507 AN: 152132 Hom.: 26072 Cov.: 32 AF XY: 0.555 AC XY: 41304 AN XY: 74370

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.611

Alfa AF: 0.674 Hom.: 36134

Bravo AF: 0.550

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.10
Dann	Benign	0.37

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: rs3748608; hg19: chr1-151551320;