2-66821029-G-A

Variant names:

• chr2-66821029-G-A
• rs11682718
• ENST00000455096.1:n.1220C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455096.1(DNMT3AP1):​n.1220C>T 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 0.0725 in 154,702 control chromosomes in the GnomAD database, including 601 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 0.073 (597 hom., cov: 32)
  • Exomes 𝑓: 0.055 (4 hom.)
• Consequence: DNMT3AP1 ENST00000455096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92
• Publications: 1 publications found

Genes affected

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

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNMT3AP1		n.66821029G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNMT3AP1	ENST00000455096.1	n.1220C>T		non_coding_transcript_exon_variant	Exon 2 of 2	6
LINC01798	ENST00000715601.1	n.185-26957G>A		intron_variant	Intron 2 of 6
LINC01798	ENST00000758432.1	n.185-26957G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11072 AN: 152102 Hom.: 595 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0694

GnomAD4 exome AF: 0.0548 AC: 136 AN: 2482 Hom.: 4 Cov.: 0 AF XY: 0.0540 AC XY: 71 AN XY: 1316

African (AFR) AF: 0.00 AC: 0 AN: 20

American (AMR) AF: 0.150 AC: 3 AN: 20

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22

East Asian (EAS) AF: 0.0556 AC: 1 AN: 18

South Asian (SAS) AF: 0.0437 AC: 9 AN: 206

European-Finnish (FIN) AF: 0.0543 AC: 38 AN: 700

Middle Eastern (MID) AF: 0.0214 AC: 6 AN: 280

European-Non Finnish (NFE) AF: 0.0672 AC: 74 AN: 1102

Other (OTH) AF: 0.0439 AC: 5 AN: 114

GnomAD4 genome AF: 0.0728 AC: 11077 AN: 152220 Hom.: 597 Cov.: 32 AF XY: 0.0758 AC XY: 5638 AN XY: 74428

African (AFR) AF: 0.0165 AC: 687 AN: 41556

American (AMR) AF: 0.148 AC: 2268 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0813 AC: 421 AN: 5176

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5905 AN: 67996

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0785 Hom.: 949

Bravo AF: 0.0711

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs11682718; hg19: chr2-67048161;