rs3732630

Variant names:

• chr3-58193301-T-A
• rs3732630
• NM_004944.4:c.801+42A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-58193301-T-A
• chr3-58193301-T-C
• chr3-58193301-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004944.4(DNASE1L3):​c.801+42A>T 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: 30)
• Consequence: DNASE1L3 NM_004944.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

DNASE1L3 (HGNC:2959): (deoxyribonuclease 1 like 3) This gene encodes a member of the deoxyribonuclease I family. The encoded protein hydrolyzes DNA, is not inhibited by actin, and mediates the breakdown of DNA during apoptosis. Mutations in this gene are a cause of systemic lupus erythematosus-16. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.068802).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNASE1L3	NM_004944.4	c.801+42A>T		intron_variant	Intron 7 of 7	ENST00000394549.7	NP_004935.1
DNASE1L3	NM_001256560.2	c.711+42A>T		intron_variant	Intron 6 of 6		NP_001243489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNASE1L3	ENST00000394549.7	c.801+42A>T		intron_variant	Intron 7 of 7	1	NM_004944.4	ENSP00000378053.2
DNASE1L3	ENST00000483681.5	c.843A>T	p.Lys281Asn	missense_variant	Exon 9 of 9	5		ENSP00000417047.1
DNASE1L3	ENST00000486455.5	c.711+42A>T		intron_variant	Intron 6 of 6	2		ENSP00000419052.1
DNASE1L3	ENST00000477209.5	c.327-498A>T		intron_variant	Intron 3 of 3	2		ENSP00000417976.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.65
DANN	Benign	0.37
Eigen	Benign	-0.98
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.19	N
LIST_S2	Benign	0.23	T
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.069	T
MetaSVM	Benign	-1.0	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.0060
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.086
MutPred		0.25		Loss of methylation at K281 (P = 0.0098);
MVP		0.13
ClinPred		0.062	T
GERP RS		-0.49

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: rs3732630; hg19: chr3-58179028;