Variant 12-63626530-TA-TAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_173812.5(DPY19L2):c.804-6_804-5dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 3465 hom., cov: 0)

Exomes 𝑓: 0.13 ( 1378 hom. )

Failed GnomAD Quality Control

Consequence

DPY19L2
NM_173812.5 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.702

Variant links:

Genes affected

DPY19L2 (HGNC:19414): (dpy-19 like 2) The protein encoded by this gene belongs to the dpy-19 family. It is highly expressed in testis, and is required for sperm head elongation and acrosome formation during spermatogenesis. Mutations in this gene are associated with an infertility disorder, spermatogenic failure type 9 (SPGF9). [provided by RefSeq, Dec 2011]

DPY19L2 links:

ENSG00000249753 (HGNC:):

ENSG00000249753 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-63626530-T-TAA is Benign according to our data. Variant chr12-63626530-T-TAA is described in ClinVar as [Benign]. Clinvar id is 402795.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPY19L2	NM_173812.5 linkuse as main transcript	c.804-6_804-5dupTT		splice_region_variant, intron_variant		ENST00000324472.9	NP_776173.3	Q6NUT2-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
DPY19L2	ENST00000324472.9 linkuse as main transcript	c.804-6_804-5dupTT	splice_region_variant, intron_variant	1	NM_173812.5	ENSP00000315988.4	Q6NUT2-1
DPY19L2	ENST00000306389.7 linkuse as main transcript	n.287-6_287-5dupTT	splice_region_variant, intron_variant	1		ENSP00000445878.1	F5H0W1
ENSG00000249753	ENST00000509615.2 linkuse as main transcript	n.239-2708_239-2707dupTT	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

28259

AN:

125954

Hom.:

3462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.235

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.225

GnomAD3 exomes

AF:

0.0800

AC:

7483

AN:

93570

Hom.:

785

AF XY:

0.0790

AC XY:

4103

AN XY:

51912

show subpopulations

Gnomad AFR exome

AF:

0.0947

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.130

Gnomad SAS exome

AF:

0.0958

Gnomad FIN exome

AF:

0.0651

Gnomad NFE exome

AF:

0.0610

Gnomad OTH exome

AF:

0.0849

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.127

AC:

140485

AN:

1110554

Hom.:

1378

Cov.:

AF XY:

0.126

AC XY:

69045

AN XY:

549214

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.114

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.168

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.0917

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.129

GnomAD4 genome

AF:

0.224

AC:

28261

AN:

125942

Hom.:

3465

Cov.:

AF XY:

0.226

AC XY:

13562

AN XY:

60076

show subpopulations

Gnomad4 AFR

AF:

0.187

Gnomad4 AMR

AF:

0.271

Gnomad4 ASJ

AF:

0.305

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.323

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.226

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over