7-29731981-A-C

Variant names:

• chr7-29731981-A-C
• rs850084
• ENST00000414296.2:n.1687A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000414296.2(DPY19L2P3):​n.1687A>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 ENST00000414296.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 8 publications found

Genes affected

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

DPY19L2P3 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DPY19L2P3	NR_158194.1	n.1175A>C		non_coding_transcript_exon_variant	Exon 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L2P3	ENST00000414296.2	n.1687A>C		non_coding_transcript_exon_variant	Exon 17 of 19	6
DPY19L2P3	ENST00000688393.1	n.792A>C		non_coding_transcript_exon_variant	Exon 11 of 12
DPY19L2P3	ENST00000689485.1	n.261A>C		non_coding_transcript_exon_variant	Exon 3 of 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

African (AFR) AF: 0.236 AC: 7214 AN: 30540

American (AMR) AF: 0.416 AC: 14496 AN: 34842

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 5019 AN: 24838

East Asian (EAS) AF: 0.333 AC: 12124 AN: 36354

South Asian (SAS) AF: 0.314 AC: 23710 AN: 75392

European-Finnish (FIN) AF: 0.305 AC: 15634 AN: 51270

Middle Eastern (MID) AF: 0.240 AC: 1340 AN: 5576

European-Non Finnish (NFE) AF: 0.253 AC: 274873 AN: 1088150

Other (OTH) AF: 0.265 AC: 15272 AN: 57678

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

African (AFR) AF: 0.249 AC: 10218 AN: 41114

American (AMR) AF: 0.394 AC: 5964 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3464

East Asian (EAS) AF: 0.315 AC: 1604 AN: 5090

South Asian (SAS) AF: 0.347 AC: 1655 AN: 4764

European-Finnish (FIN) AF: 0.310 AC: 3203 AN: 10340

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17544 AN: 67814

Other (OTH) AF: 0.290 AC: 605 AN: 2086

Alfa AF: 0.269 Hom.: 6773

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs850084; hg19: chr7-29771597;