rs3892630

Variant names:

• chr19-32690578-C-T
• rs3892630
• ENST00000592431.4:n.672+785G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592431.4(NUDT19-DT):​n.672+785G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,108 control chromosomes in the GnomAD database, including 3,003 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 0.19 (3003 hom., cov: 32)
• Consequence: NUDT19-DT ENST00000592431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 33 publications found

Genes affected

NUDT19-DT (HGNC:55296): (NUDT19 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT19-DT	NR_186320.1	n.934+785G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT19-DT	ENST00000592431.4	n.672+785G>A		intron_variant	Intron 1 of 1	2
NUDT19-DT	ENST00000702394.2	n.165+1026G>A		intron_variant	Intron 1 of 1
NUDT19-DT	ENST00000789913.1	n.464-3310G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29065 AN: 151990 Hom.: 2999 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.191 AC: 29080 AN: 152108 Hom.: 3003 Cov.: 32 AF XY: 0.191 AC XY: 14224 AN XY: 74354

African (AFR) AF: 0.259 AC: 10730 AN: 41484

American (AMR) AF: 0.136 AC: 2081 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1023 AN: 5172

South Asian (SAS) AF: 0.120 AC: 577 AN: 4820

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10566

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11107 AN: 68004

Other (OTH) AF: 0.180 AC: 379 AN: 2108

Alfa AF: 0.172 Hom.: 8219

Bravo AF: 0.189

Asia WGS AF: 0.189 AC: 655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.9
DANN	Benign	0.88
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3892630; hg19: chr19-33181484;