2-25266314-G-C

Position:

• chr2-25266314-G-C

Variant summary

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

The NM_022552.5(DNMT3A):​c.639+8627C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,058 control chromosomes in the GnomAD database, including 19,189 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 0.50 (19189 hom., cov: 32)
• Consequence: DNMT3A NM_022552.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

DNMT3A (HGNC:2978): (DNA methyltransferase 3 alpha) CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase that is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes to the cytoplasm and nucleus and its expression is developmentally regulated. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNMT3A	NM_022552.5	c.639+8627C>G		intron_variant		ENST00000321117.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNMT3A	ENST00000321117.10	c.639+8627C>G		intron_variant		1	NM_022552.5	P3
DNMT3A	ENST00000264709.7	c.639+8627C>G		intron_variant		1		P3
DNMT3A	ENST00000380756.7	c.639+8627C>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75624 AN: 151940 Hom.: 19188 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.498 AC: 75652 AN: 152058 Hom.: 19189 Cov.: 32 AF XY: 0.494 AC XY: 36734 AN XY: 74332

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.500

Alfa AF: 0.388 Hom.: 1050

Bravo AF: 0.486

Asia WGS AF: 0.340 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7590760; hg19: chr2-25489183;