NM_030625.3:c.*900C>T

Variant names:

• chr10-68692714-C-T
• rs5030882
• NM_030625.3:c.*900C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030625.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TET1	NM_030625.3	MANE Select	c.*900C>T		3_prime_UTR	Exon 12 of 12	NP_085128.2	Q8NFU7-1
	TET1	NM_001406365.1		c.*900C>T		3_prime_UTR	Exon 13 of 13	NP_001393294.1
	TET1	NM_001406367.1		c.*900C>T		3_prime_UTR	Exon 12 of 12	NP_001393296.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TET1	ENST00000373644.5	TSL:1 MANE Select	c.*900C>T		3_prime_UTR	Exon 12 of 12	ENSP00000362748.4	Q8NFU7-1
	TET1	ENST00000929765.1		c.*900C>T		3_prime_UTR	Exon 14 of 14	ENSP00000599824.1
	TET1	ENST00000929763.1		c.*900C>T		3_prime_UTR	Exon 13 of 13	ENSP00000599822.1

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

African (AFR) AF: 0.785 AC: 2988 AN: 3806

American (AMR) AF: 0.931 AC: 2270 AN: 2438

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 4686 AN: 5002

East Asian (EAS) AF: 0.988 AC: 10792 AN: 10926

South Asian (SAS) AF: 0.928 AC: 633 AN: 682

European-Finnish (FIN) AF: 0.958 AC: 69 AN: 72

Middle Eastern (MID) AF: 0.932 AC: 440 AN: 472

European-Non Finnish (NFE) AF: 0.939 AC: 45737 AN: 48726

Other (OTH) AF: 0.925 AC: 6111 AN: 6604

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

African (AFR) AF: 0.771 AC: 31952 AN: 41420

American (AMR) AF: 0.910 AC: 13898 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3261 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5077 AN: 5186

South Asian (SAS) AF: 0.937 AC: 4519 AN: 4822

European-Finnish (FIN) AF: 0.985 AC: 10436 AN: 10600

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64021 AN: 68002

Other (OTH) AF: 0.892 AC: 1884 AN: 2112

Alfa AF: 0.927 Hom.: 75446

Bravo AF: 0.885

Asia WGS AF: 0.938 AC: 3259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.055
DANN	Benign	0.46
PhyloP100		-0.70
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: rs5030882; hg19: chr10-70452471;