Variant rs2738822 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_005618.4(DLL1):c.670+51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,612,078 control chromosomes in the GnomAD database, including 267,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 21214 hom., cov: 33)

Exomes 𝑓: 0.57 ( 246435 hom. )

Consequence

DLL1
NM_005618.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.330

Variant links:

Genes affected

DLL1 (HGNC:2908): (delta like canonical Notch ligand 1) DLL1 is a human homolog of the Notch Delta ligand and is a member of the delta/serrate/jagged family. It plays a role in mediating cell fate decisions during hematopoiesis. It may play a role in cell-to-cell communication. [provided by RefSeq, Jul 2008]

DLL1 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 (BayesDel_noAF=-0.84).

BP6

Variant 6-170288188-C-T is Benign according to our data. Variant chr6-170288188-C-T is described in ClinVar as [Benign]. Clinvar id is 1253770.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLL1	NM_005618.4 linkuse as main transcript	c.670+51G>A		intron_variant		ENST00000366756.4	NP_005609.3
DLL1	XM_005266934.5 linkuse as main transcript	c.670+51G>A		intron_variant			XP_005266991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLL1	ENST00000366756.4 linkuse as main transcript	c.670+51G>A		intron_variant		1	NM_005618.4	ENSP00000355718	P1	O00548-1

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78259

AN:

151970

Hom.:

21203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.623

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.0738

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.551

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.598

Gnomad OTH

AF:

0.529

GnomAD3 exomes

AF:

0.511

AC:

126531

AN:

247400

Hom.:

34919

AF XY:

0.518

AC XY:

69493

AN XY:

134200

show subpopulations

Gnomad AFR exome

AF:

0.404

Gnomad AMR exome

AF:

0.511

Gnomad ASJ exome

AF:

0.583

Gnomad EAS exome

AF:

0.0669

Gnomad SAS exome

AF:

0.464

Gnomad FIN exome

AF:

0.531

Gnomad NFE exome

AF:

0.601

Gnomad OTH exome

AF:

0.555

GnomAD4 exome

AF:

0.572

AC:

834642

AN:

1459990

Hom.:

246435

Cov.:

AF XY:

0.570

AC XY:

413903

AN XY:

726290

show subpopulations

Gnomad4 AFR exome

AF:

0.411

Gnomad4 AMR exome

AF:

0.514

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.0553

Gnomad4 SAS exome

AF:

0.470

Gnomad4 FIN exome

AF:

0.534

Gnomad4 NFE exome

AF:

0.608

Gnomad4 OTH exome

AF:

0.551

GnomAD4 genome

AF:

0.515

AC:

78307

AN:

152088

Hom.:

21214

Cov.:

AF XY:

0.510

AC XY:

37911

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.412

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.593

Gnomad4 EAS

AF:

0.0746

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.551

Gnomad4 NFE

AF:

0.598

Gnomad4 OTH

AF:

0.525

Alfa

AF:

0.560

Hom.:

4433

Bravo

AF:

0.509

Asia WGS

AF:

0.253

AC:

885

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

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

DANN

Benign

0.87

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