2-66821463-T-C

Variant summary

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

The ENST00000455096.1(DNMT3AP1):n.786A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,080 control chromosomes in the GnomAD database, including 21,747 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 0.53 (21729 hom., cov: 32)
  • Exomes 𝑓: 0.54 (18 hom.)
• Consequence: DNMT3AP1 ENST00000455096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

Genes affected

DNMT3AP1 (HGNC:23164): (DNA methyltransferase 3A pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNMT3AP1	ENST00000455096.1	n.786A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80732 AN: 151852 Hom.: 21696 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.488

GnomAD4 exome AF: 0.537 AC: 58 AN: 108 Hom.: 18 Cov.: 0 AF XY: 0.541 AC XY: 40 AN XY: 74

Gnomad4 AFR exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.533

Gnomad4 NFE exome AF: 0.563

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.532 AC: 80817 AN: 151972 Hom.: 21729 Cov.: 32 AF XY: 0.538 AC XY: 39947 AN XY: 74258

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.491

Alfa AF: 0.517 Hom.: 7326

Bravo AF: 0.537

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.5
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: rs1106577; hg19: chr2-67048595;