Variant 18-49044292-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001353214.3(DYM):c.2026-88G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 1,488,718 control chromosomes in the GnomAD database, including 5,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.072 ( 436 hom., cov: 33)

Exomes 𝑓: 0.081 ( 4754 hom. )

Consequence

DYM
NM_001353214.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.202

Variant links:

Genes affected

DYM (HGNC:21317): (dymeclin) This gene encodes a protein which regulates Golgi-associated secretory pathways that are essential to endochondral bone formation during early development. This gene is also believed to play a role in early brain development. This gene is widely expressed in embryos and is particularly abundant in chodrocytes and brain tissues. It encodes a peripheral membrane protein which shuttles between the cytosol and Golgi complex. Mutations in this gene are associated with two types of recessive osteochondrodysplasia: Dyggve-Melchior-Clausen (DMC) dysplasia and Smith-McCort (SMC) dysplasia. [provided by RefSeq, Jun 2017]

DYM links:

DYM-AS1 (HGNC:37046): (DYM antisense RNA 1)

DYM-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 18-49044292-C-T is Benign according to our data. Variant chr18-49044292-C-T is described in ClinVar as [Benign]. Clinvar id is 1265453.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYM	NM_001353214.3 linkuse as main transcript	c.2026-88G>A		intron_variant		ENST00000675505.1
DYM-AS1	NR_148999.1 linkuse as main transcript	n.313-3836C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYM	ENST00000675505.1 linkuse as main transcript	c.2026-88G>A		intron_variant			NM_001353214.3
DYM-AS1	ENST00000584252.1 linkuse as main transcript	n.313-3836C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0723

AC:

10995

AN:

152036

Hom.:

435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0586

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0750

Gnomad ASJ

AF:

0.0871

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.0657

Gnomad FIN

AF:

0.0519

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.0878

Gnomad OTH

AF:

0.0929

GnomAD4 exome

AF:

0.0808

AC:

107943

AN:

1336564

Hom.:

4754

AF XY:

0.0808

AC XY:

54216

AN XY:

670976

show subpopulations

Gnomad4 AFR exome

AF:

0.0609

Gnomad4 AMR exome

AF:

0.0547

Gnomad4 ASJ exome

AF:

0.0819

Gnomad4 EAS exome

AF:

0.00108

Gnomad4 SAS exome

AF:

0.0705

Gnomad4 FIN exome

AF:

0.0488

Gnomad4 NFE exome

AF:

0.0877

Gnomad4 OTH exome

AF:

0.0811

GnomAD4 genome

AF:

0.0723

AC:

10997

AN:

152154

Hom.:

436

Cov.:

AF XY:

0.0696

AC XY:

5175

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0586

Gnomad4 AMR

AF:

0.0749

Gnomad4 ASJ

AF:

0.0871

Gnomad4 EAS

AF:

0.00309

Gnomad4 SAS

AF:

0.0651

Gnomad4 FIN

AF:

0.0519

Gnomad4 NFE

AF:

0.0878

Gnomad4 OTH

AF:

0.0919

Alfa

AF:

0.0835

Hom.:

Bravo

AF:

0.0726

Asia WGS

AF:

0.0360

AC:

124

AN:

3478

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

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

Cadd

Benign

0.84

Dann

Benign

0.43

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