10-68692714-C-T

Position:

• chr10-68692714-C-T

Variant summary

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

The NM_030625.3(TET1):​c.*900C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 230,822 control chromosomes in the GnomAD database, including 96,041 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 0.90 (61471 hom., cov: 30)
  • Exomes 𝑓: 0.94 (34570 hom.)
• Consequence: TET1 NM_030625.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

Genes affected

TET1 (HGNC:29484): (tet methylcytosine dioxygenase 1) DNA methylation is an epigenetic mechanism that is important for controlling gene expression. The protein encoded by this gene is a demethylase that belongs to the TET (ten-eleven translocation) family. Members of the TET protein family play a role in the DNA methylation process and gene activation. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TET1	NM_030625.3	c.*900C>T		3_prime_UTR_variant	12/12	ENST00000373644.5	NP_085128.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TET1	ENST00000373644.5	c.*900C>T		3_prime_UTR_variant	12/12	1	NM_030625.3	ENSP00000362748.4

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136097 AN: 151976 Hom.: 61433 Cov.: 30

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.890

GnomAD4 exome AF: 0.936 AC: 73726 AN: 78728 Hom.: 34570 Cov.: 0 AF XY: 0.937 AC XY: 33944 AN XY: 36212

Gnomad4 AFR exome AF: 0.785

Gnomad4 AMR exome AF: 0.931

Gnomad4 ASJ exome AF: 0.937

Gnomad4 EAS exome AF: 0.988

Gnomad4 SAS exome AF: 0.928

Gnomad4 FIN exome AF: 0.958

Gnomad4 NFE exome AF: 0.939

Gnomad4 OTH exome AF: 0.925

GnomAD4 genome AF: 0.895 AC: 136189 AN: 152094 Hom.: 61471 Cov.: 30 AF XY: 0.898 AC XY: 66756 AN XY: 74368

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.892

Alfa AF: 0.930 Hom.: 63890

Bravo AF: 0.885

Asia WGS AF: 0.938 AC: 3259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.055
DANN	Benign	0.46

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: rs5030882; hg19: chr10-70452471;