rs6587597

Positions:

• chr1-151548255-A-G
• chr1-151548255-A-T

Variant summary

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

The NM_020127.3(TUFT1):​c.60+7829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 150,540 control chromosomes in the GnomAD database, including 9,113 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 0.33 (9113 hom., cov: 31)
• Consequence: TUFT1 NM_020127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUFT1	NM_020127.3	c.60+7829A>G		intron_variant		ENST00000368849.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUFT1	ENST00000368849.8	c.60+7829A>G		intron_variant		1	NM_020127.3	A1
	ENST00000434112.1	n.394+7346A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.331 AC: 49856 AN: 150466 Hom.: 9100 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.331 AC: 49886 AN: 150540 Hom.: 9113 Cov.: 31 AF XY: 0.342 AC XY: 25110 AN XY: 73390

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.370

Alfa AF: 0.328 Hom.: 4347

Bravo AF: 0.328

Asia WGS AF: 0.431 AC: 1500 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	3.2
DANN	Benign	0.56

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: rs6587597; hg19: chr1-151520731;