Variant chr10-80362513-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_032372.6(DYDC2):c.70G>T(p.Val24Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,614,094 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 17 hom., cov: 33)

Exomes 𝑓: 0.00083 ( 10 hom. )

Consequence

DYDC2
NM_032372.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.91

Variant links:

Genes affected

DYDC2 (HGNC:23468): (DPY30 domain containing 2) This gene encodes a member of a family of proteins that contains a DPY30 domain. This gene locus overlaps with a closely related gene on the opposite strand. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

DYDC2 links:

DYDC2 (HGNC:):

DYDC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0151591).

BP6

Variant 10-80362513-G-T is Benign according to our data. Variant chr10-80362513-G-T is described in ClinVar as [Benign]. Clinvar id is 709982.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00696 (1060/152294) while in subpopulation AFR AF= 0.0239 (994/41562). AF 95% confidence interval is 0.0227. There are 17 homozygotes in gnomad4. There are 509 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYDC2	NM_032372.6 linkuse as main transcript	c.70G>T	p.Val24Phe	missense_variant	3/5	ENST00000256039.3	NP_115748.1	Q96IM9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYDC2	ENST00000256039.3 linkuse as main transcript	c.70G>T	p.Val24Phe	missense_variant	3/5	2	NM_032372.6	ENSP00000256039.2		Q96IM9

Frequencies

GnomAD3 genomes

AF:

0.00698

AC:

1062

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00210

AC:

529

AN:

251406

Hom.:

AF XY:

0.00157

AC XY:

213

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.0239

Gnomad AMR exome

AF:

0.00113

Gnomad ASJ exome

AF:

0.00724

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000123

Gnomad OTH exome

AF:

0.00245

GnomAD4 exome

AF:

0.000828

AC:

1211

AN:

1461800

Hom.:

Cov.:

AF XY:

0.000703

AC XY:

511

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.0232

Gnomad4 AMR exome

AF:

0.00125

Gnomad4 ASJ exome

AF:

0.00689

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000348

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000612

Gnomad4 OTH exome

AF:

0.00205

GnomAD4 genome

AF:

0.00696

AC:

1060

AN:

152294

Hom.:

Cov.:

AF XY:

0.00683

AC XY:

509

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0239

Gnomad4 AMR

AF:

0.00203

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000176

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00164

Hom.:

Bravo

AF:

0.00764

ESP6500AA

AF:

0.0247

AC:

109

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.00241

AC:

292

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000237

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.086

T;T;T;T;T;T;T

Eigen

Uncertain

0.28

Eigen_PC

Benign

0.14

FATHMM_MKL

Benign

0.097

LIST_S2

Uncertain

0.86

.;D;.;D;.;D;.

MetaRNN

Benign

0.015

T;T;T;T;T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Uncertain

2.2

M;.;M;M;M;.;M

PrimateAI

Benign

0.35

PROVEAN

Benign

-2.4

N;N;N;N;.;N;N

REVEL

Benign

0.23

Sift

Benign

0.44

T;T;T;T;.;T;T

Sift4G

Benign

0.61

T;T;T;T;T;T;T

Polyphen

1.0

D;.;D;D;D;.;D

Vest4

0.25

MVP

0.72

MPC

0.58

ClinPred

0.043

GERP RS

3.5

Varity_R

0.12

gMVP

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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