rs12984523

chr19-10196143-C-T

Variant summary

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

The ENST00000588118.5(DNMT1):c.11-1089G>A 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 152,036 control chromosomes in the GnomAD database, including 18,303 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 (18303 hom., cov: 32)
• Consequence: DNMT1 ENST00000588118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

Genes affected

DNMT1 (HGNC:2976): (DNA methyltransferase 1) This gene encodes an enzyme that transfers methyl groups to cytosine nucleotides of genomic DNA. This protein is the major enzyme responsible for maintaining methylation patterns following DNA replication and shows a preference for hemi-methylated DNA. Methylation of DNA is an important component of mammalian epigenetic gene regulation. Aberrant methylation patterns are found in human tumors and associated with developmental abnormalities. Variation in this gene has been associated with cerebellar ataxia, deafness, and narcolepsy, and neuropathy, hereditary sensory, type IE. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 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
DNMT1	ENST00000586800.5	c.-284+4731G>A		intron_variant		3
DNMT1	ENST00000588118.5	c.11-1089G>A		intron_variant		5
DNMT1	ENST00000588952.5	c.-283-14066G>A		intron_variant		5
DNMT1	ENST00000592342.5	c.-283-14066G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74106 AN: 151918 Hom.: 18308 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.488 AC: 74127 AN: 152036 Hom.: 18303 Cov.: 32 AF XY: 0.486 AC XY: 36140 AN XY: 74328

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.509

Alfa AF: 0.500 Hom.: 2346

Bravo AF: 0.493

Asia WGS AF: 0.392 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12984523; hg19: chr19-10306819;