rs850084

chr7-29731981-A-Cchr7-29731981-A-Gchr7-29731981-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_158194.1(DPY19L2P3):n.1175A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,555,664 control chromosomes in the GnomAD database, including 56,589 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 0.28 (6078 hom., cov: 29)
  • Exomes 𝑓: 0.26 (50511 hom.)
• Consequence: DPY19L2P3 NR_158194.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

Genes affected

DPY19L2P3 (HGNC:22367): (DPY19L2 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L2P3	NR_158194.1	n.1175A>C		non_coding_transcript_exon_variant	7/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L2P3	ENST00000414296.2	n.1687A>C		non_coding_transcript_exon_variant	17/19
DPY19L2P3	ENST00000688393.1	n.792A>C		non_coding_transcript_exon_variant	11/12
DPY19L2P3	ENST00000689485.1	n.261A>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41803 AN: 150908 Hom.: 6082 Cov.: 29

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.283

GnomAD4 exome AF: 0.263 AC: 369682 AN: 1404640 Hom.: 50511 Cov.: 35 AF XY: 0.264 AC XY: 183967 AN XY: 697310

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.416

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.314

Gnomad4 FIN exome AF: 0.305

Gnomad4 NFE exome AF: 0.253

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.277 AC: 41821 AN: 151024 Hom.: 6078 Cov.: 29 AF XY: 0.284 AC XY: 20899 AN XY: 73694

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.290

Alfa AF: 0.267 Hom.: 5772

Bravo AF: 0.282

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	7.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs850084; hg19: chr7-29771597;