Variant chr11-126304143-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014026.6(DCPS):c.63C>T(p.His21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 1,614,040 control chromosomes in the GnomAD database, including 3,059 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.049 ( 346 hom., cov: 33)

Exomes 𝑓: 0.048 ( 2713 hom. )

Consequence

DCPS
NM_014026.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.117

Variant links:

Genes affected

DCPS (HGNC:29812): (decapping enzyme, scavenger) This gene encodes a member of the histidine triad family of pyrophosphatases that removes short mRNA fragments containing the 5′ mRNA cap structure, which appear in the 3′ → 5′ mRNA decay pathway, following deadenylation and exosome-mediated turnover. This enzyme hydrolyzes the triphosphate linkage of the cap structure (7-methylguanosine nucleoside triphosphate) to yield 7-methylguanosine monophosphate and nucleoside diphosphate. It protects the cell from the potentially toxic accumulation of these short, capped mRNA fragments, and regulates the activity of other cap-binding proteins, which are inhibited by their accumulation. It also acts as a transcript-specific modulator of pre-mRNA splicing and microRNA turnover. [provided by RefSeq, Apr 2017]

DCPS links:

TIRAP-AS1 (HGNC:56069): (TIRAP antisense RNA 1)

TIRAP-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 11-126304143-C-T is Benign according to our data. Variant chr11-126304143-C-T is described in ClinVar as [Benign]. Clinvar id is 1229271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.117 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCPS	NM_014026.6 linkuse as main transcript	c.63C>T	p.His21=	synonymous_variant	1/6	ENST00000263579.5
DCPS	NM_001350236.2 linkuse as main transcript	c.63C>T	p.His21=	synonymous_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DCPS	ENST00000263579.5 linkuse as main transcript	c.63C>T	p.His21=	synonymous_variant	1/6	1	NM_014026.6	P1
TIRAP-AS1	ENST00000524964.2 linkuse as main transcript	n.116+65G>A		intron_variant, non_coding_transcript_variant		2
TIRAP-AS1	ENST00000693424.1 linkuse as main transcript	n.157G>A		non_coding_transcript_exon_variant	1/1
TIRAP-AS1	ENST00000691542.1 linkuse as main transcript	n.114+65G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0488

AC:

7434

AN:

152222

Hom.:

345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00911

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.0799

Gnomad FIN

AF:

0.0672

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0411

Gnomad OTH

AF:

0.0544

GnomAD3 exomes

AF:

0.0739

AC:

18529

AN:

250802

Hom.:

1171

AF XY:

0.0699

AC XY:

9478

AN XY:

135688

show subpopulations

Gnomad AFR exome

AF:

0.00887

Gnomad AMR exome

AF:

0.186

Gnomad ASJ exome

AF:

0.0367

Gnomad EAS exome

AF:

0.167

Gnomad SAS exome

AF:

0.0681

Gnomad FIN exome

AF:

0.0689

Gnomad NFE exome

AF:

0.0403

Gnomad OTH exome

AF:

0.0627

GnomAD4 exome

AF:

0.0481

AC:

70268

AN:

1461700

Hom.:

2713

Cov.:

AF XY:

0.0485

AC XY:

35295

AN XY:

727150

show subpopulations

Gnomad4 AFR exome

AF:

0.00696

Gnomad4 AMR exome

AF:

0.175

Gnomad4 ASJ exome

AF:

0.0376

Gnomad4 EAS exome

AF:

0.168

Gnomad4 SAS exome

AF:

0.0696

Gnomad4 FIN exome

AF:

0.0679

Gnomad4 NFE exome

AF:

0.0374

Gnomad4 OTH exome

AF:

0.0504

GnomAD4 genome

AF:

0.0489

AC:

7444

AN:

152340

Hom.:

346

Cov.:

AF XY:

0.0534

AC XY:

3975

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00909

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.0337

Gnomad4 EAS

AF:

0.171

Gnomad4 SAS

AF:

0.0789

Gnomad4 FIN

AF:

0.0672

Gnomad4 NFE

AF:

0.0411

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0409

Hom.:

264

Bravo

AF:

0.0505

Asia WGS

AF:

0.140

AC:

486

AN:

3478

EpiCase

AF:

0.0393

EpiControl

AF:

0.0394

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

Nov 16, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.2

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

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