19-10174102-A-G

Variant names:

• chr19-10174102-A-G
• rs759920
• NM_001130823.3:c.649-197T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001130823.3(DNMT1):​c.649-197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,940 control chromosomes in the GnomAD database, including 20,149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.51 (20149 hom., cov: 31)
• Consequence: DNMT1 NM_001130823.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.691

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 19-10174102-A-G is Benign according to our data. Variant chr19-10174102-A-G is described in ClinVar as [Benign]. Clinvar id is 679318.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNMT1	NM_001130823.3	c.649-197T>C		intron_variant	Intron 7 of 40	ENST00000359526.9	NP_001124295.1
DNMT1	NM_001318730.2	c.601-197T>C		intron_variant	Intron 6 of 39		NP_001305659.1
DNMT1	NM_001379.4	c.601-197T>C		intron_variant	Intron 6 of 39		NP_001370.1
DNMT1	NM_001318731.2	c.286-197T>C		intron_variant	Intron 7 of 40		NP_001305660.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNMT1	ENST00000359526.9	c.649-197T>C		intron_variant	Intron 7 of 40	1	NM_001130823.3	ENSP00000352516.3

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77691 AN: 151822 Hom.: 20116 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.512 AC: 77788 AN: 151940 Hom.: 20149 Cov.: 31 AF XY: 0.513 AC XY: 38107 AN XY: 74264

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.492

Alfa AF: 0.406 Hom.: 1568

Bravo AF: 0.506

Asia WGS AF: 0.606 AC: 2105 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.65

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: rs759920; hg19: chr19-10284778; COSMIC: COSV61584146; COSMIC: COSV61584146;