rs8106605

Positions:

• chr19-10212956-T-G

Variant summary

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

The ENST00000588952.5(DNMT1):​c.-284+5796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,126 control chromosomes in the GnomAD database, including 2,039 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 0.16 (2039 hom., cov: 31)
• Consequence: DNMT1 ENST00000588952.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNMT1	ENST00000588952.5	c.-284+5796A>C		intron_variant		5		ENSP00000467050
DNMT1	ENST00000592342.5	c.-284+18248A>C		intron_variant		3		ENSP00000465993

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24294 AN: 152008 Hom.: 2043 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.160 AC: 24284 AN: 152126 Hom.: 2039 Cov.: 31 AF XY: 0.156 AC XY: 11621 AN XY: 74390

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.177

Alfa AF: 0.151 Hom.: 227

Bravo AF: 0.166

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8106605; hg19: chr19-10323632;