rs2162560

Positions:

• chr19-10168778-G-A

Variant summary

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

The NM_001130823.3(DNMT1):​c.769-414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,994 control chromosomes in the GnomAD database, including 10,048 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 0.35 (10048 hom., cov: 32)
• Consequence: DNMT1 NM_001130823.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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]

DNMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNMT1	NM_001130823.3	c.769-414C>T		intron_variant		ENST00000359526.9	NP_001124295.1
DNMT1	NM_001318730.2	c.721-414C>T		intron_variant			NP_001305659.1
DNMT1	NM_001379.4	c.721-414C>T		intron_variant			NP_001370.1
DNMT1	NM_001318731.2	c.406-414C>T		intron_variant			NP_001305660.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNMT1	ENST00000359526.9	c.769-414C>T		intron_variant		1	NM_001130823.3	ENSP00000352516.3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53333 AN: 151876 Hom.: 10049 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.351 AC: 53345 AN: 151994 Hom.: 10048 Cov.: 32 AF XY: 0.346 AC XY: 25691 AN XY: 74296

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.349

Alfa AF: 0.411 Hom.: 7683

Bravo AF: 0.335

Asia WGS AF: 0.279 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2162560; hg19: chr19-10279454;