rs13401241

Positions:

• chr2-25295601-C-A
• chr2-25295601-C-G

Variant summary

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

The NM_022552.5(DNMT3A):​c.177+4538G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,090 control chromosomes in the GnomAD database, including 18,605 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 0.49 (18605 hom., cov: 33)
• Consequence: DNMT3A NM_022552.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNMT3A	NM_022552.5	c.177+4538G>T		intron_variant		ENST00000321117.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNMT3A	ENST00000321117.10	c.177+4538G>T		intron_variant		1	NM_022552.5	P3
DNMT3A	ENST00000264709.7	c.177+4538G>T		intron_variant		1		P3
DNMT3A	ENST00000406659.3	c.177+4538G>T		intron_variant		1
DNMT3A	ENST00000380756.7	c.177+4538G>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74216 AN: 151972 Hom.: 18590 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.488 AC: 74259 AN: 152090 Hom.: 18605 Cov.: 33 AF XY: 0.487 AC XY: 36182 AN XY: 74348

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.486

Alfa AF: 0.526 Hom.: 35543

Bravo AF: 0.475

Asia WGS AF: 0.335 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13401241; hg19: chr2-25518470;