rs2838535

Variant names:

• chr21-44261696-C-G
• rs2838535
• NM_175867.3:c.-8+44G>C

Your query was ambiguous. Multiple possible variants found:

• chr21-44261696-C-G
• chr21-44261696-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_175867.3(DNMT3L):​c.-8+44G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DNMT3L NM_175867.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 4 publications found

Genes affected

DNMT3L (HGNC:2980): (DNA methyltransferase 3 like) CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a nuclear protein with similarity to DNA methyltransferases, but is not thought to function as a DNA methyltransferase as it does not contain the amino acid residues necessary for methyltransferase activity. However, it does stimulate de novo methylation by DNA cytosine methyltransferase 3 alpha and is thought to be required for the establishment of maternal genomic imprints. This protein also mediates transcriptional repression through interaction with histone deacetylase 1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNMT3L	NM_175867.3	c.-8+44G>C		intron_variant	Intron 1 of 11	ENST00000628202.3	NP_787063.1
DNMT3L	NM_013369.4	c.-8+44G>C		intron_variant	Intron 1 of 11		NP_037501.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNMT3L	ENST00000628202.3	c.-8+44G>C		intron_variant	Intron 1 of 11	1	NM_175867.3	ENSP00000486001.1
DNMT3L	ENST00000270172.7	c.-8+44G>C		intron_variant	Intron 1 of 11	1		ENSP00000270172.3
DNMT3L	ENST00000431166.1	c.-8+44G>C		intron_variant	Intron 1 of 8	5		ENSP00000400242.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 15744 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8258

African (AFR) AF: 0.00 AC: 0 AN: 292

American (AMR) AF: 0.00 AC: 0 AN: 1790

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 322

East Asian (EAS) AF: 0.00 AC: 0 AN: 622

South Asian (SAS) AF: 0.00 AC: 0 AN: 1564

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 510

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 46

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 9770

Other (OTH) AF: 0.00 AC: 0 AN: 828

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.70
PhyloP100		-2.7
PromoterAI		-0.010	Neutral

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

Other links and lift over

dbSNP: rs2838535; hg19: chr21-45681579;