ENST00000426647.2:n.641-289T>G

Variant names:

• chr7-32827111-T-G
• rs2392147
• ENST00000426647.2:n.641-289T>G

Variant summary

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

The ENST00000426647.2(DPY19L1P2):​n.641-289T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,024 control chromosomes in the GnomAD database, including 19,565 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 0.49 (19565 hom., cov: 32)
• Consequence: DPY19L1P2 ENST00000426647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 18 publications found

Genes affected

DPY19L1P2 (HGNC:22851): (DPY19L1 pseudogene 2)

ENSG00000293076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426647.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L1P2	NR_132360.1		n.172-283T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L1P2	ENST00000426647.2	TSL:6	n.641-289T>G		intron	N/A
	ENSG00000293076	ENST00000720420.1		n.181-5897T>G		intron	N/A
	ENSG00000293076	ENST00000720421.1		n.152-5897T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74798 AN: 151906 Hom.: 19536 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.493 AC: 74878 AN: 152024 Hom.: 19565 Cov.: 32 AF XY: 0.494 AC XY: 36719 AN XY: 74324

African (AFR) AF: 0.675 AC: 27998 AN: 41456

American (AMR) AF: 0.396 AC: 6052 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3470

East Asian (EAS) AF: 0.570 AC: 2939 AN: 5156

South Asian (SAS) AF: 0.556 AC: 2680 AN: 4824

European-Finnish (FIN) AF: 0.425 AC: 4496 AN: 10568

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27847 AN: 67962

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.433 Hom.: 57176

Bravo AF: 0.496

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2392147;

hg19: chr7-32866723;