rs6587597

Variant names:

• chr1-151548255-A-G
• rs6587597
• NM_020127.3:c.60+7829A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

TUFT1 Gene-Disease associations (from GenCC):

• woolly hair-skin fragility syndrome

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ENSG00000232536 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TUFT1	NM_020127.3	c.60+7829A>G		intron_variant	Intron 1 of 12	ENST00000368849.8	NP_064512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUFT1	ENST00000368849.8	c.60+7829A>G		intron_variant	Intron 1 of 12	1	NM_020127.3	ENSP00000357842.3

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

African (AFR) AF: 0.203 AC: 8308 AN: 40900

American (AMR) AF: 0.470 AC: 7143 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1785 AN: 3464

East Asian (EAS) AF: 0.630 AC: 3208 AN: 5094

South Asian (SAS) AF: 0.320 AC: 1518 AN: 4748

European-Finnish (FIN) AF: 0.454 AC: 4661 AN: 10260

Middle Eastern (MID) AF: 0.359 AC: 102 AN: 284

European-Non Finnish (NFE) AF: 0.329 AC: 22228 AN: 67616

Other (OTH) AF: 0.370 AC: 771 AN: 2084

Alfa AF: 0.329 Hom.: 4834

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
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6587597; hg19: chr1-151520731;