rs2647264

Positions:

• chr4-105347437-A-G

Variant summary

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

The NR_126420.1(TET2-AS1):​n.202+5243T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,330 control chromosomes in the GnomAD database, including 420 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 0.063 (420 hom., cov: 32)
• Consequence: TET2-AS1 NR_126420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

Genes affected

TET2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TET2-AS1	NR_126420.1	n.202+5243T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9615 AN: 152212 Hom.: 420 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0631 AC: 9608 AN: 152330 Hom.: 420 Cov.: 32 AF XY: 0.0628 AC XY: 4679 AN XY: 74496

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0393

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0835 Hom.: 271

Bravo AF: 0.0621

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2647264; hg19: chr4-106268594;