7-32827111-T-G

Variant names:

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

Variant summary

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

The NR_132360.1(DPY19L1P2):​n.172-283T>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 NR_132360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1P2	NR_132360.1	n.172-283T>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1P2	ENST00000426647.2	n.641-289T>G		intron_variant	Intron 7 of 8	6

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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.477

Alfa AF: 0.422 Hom.: 28990

Bravo AF: 0.496

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2392147; hg19: chr7-32866723;