rs3892630

chr19-32690578-C-T

Variant summary

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

The ENST00000592431.3(NUDT19-DT):n.402+785G>A variant causes a intron, non coding transcript 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 ENST00000592431.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUDT19-DT	ENST00000592431.3	n.402+785G>A		intron_variant, non_coding_transcript_variant		2
NUDT19-DT	ENST00000702394.1	n.97+1026G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.180

Alfa AF: 0.166 Hom.: 2706

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3892630; hg19: chr19-33181484;