Variant 6-170282835-T-G 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.*39A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,613,400 control chromosomes in the GnomAD database, including 87,261 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6328 hom., cov: 34)

Exomes 𝑓: 0.33 ( 80933 hom. )

Consequence

DLL1
NM_005618.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.34

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=-0.78).

BP6

Variant 6-170282835-T-G is Benign according to our data. Variant chr6-170282835-T-G is described in ClinVar as [Benign]. Clinvar id is 1267364.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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.*39A>C		3_prime_UTR_variant	11/11	ENST00000366756.4	NP_005609.3	O00548-1A0A384P5C6
DLL1	XM_005266934.5 linkuse as main transcript	c.*39A>C		3_prime_UTR_variant	11/11		XP_005266991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLL1	ENST00000366756 linkuse as main transcript	c.*39A>C		3_prime_UTR_variant	11/11	1	NM_005618.4	ENSP00000355718.3		O00548-1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42640

AN:

152056

Hom.:

6330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.295

GnomAD3 exomes

AF:

0.276

AC:

69476

AN:

251466

Hom.:

10284

AF XY:

0.284

AC XY:

38540

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.205

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.265

Gnomad EAS exome

AF:

0.222

Gnomad SAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.341

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.329

AC:

480116

AN:

1461226

Hom.:

80933

Cov.:

AF XY:

0.327

AC XY:

237917

AN XY:

726948

show subpopulations

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.269

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.355

Gnomad4 OTH exome

AF:

0.312

GnomAD4 genome

AF:

0.280

AC:

42641

AN:

152174

Hom.:

6328

Cov.:

AF XY:

0.268

AC XY:

19969

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.250

Gnomad4 ASJ

AF:

0.273

Gnomad4 EAS

AF:

0.241

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.329

Hom.:

12427

Bravo

AF:

0.282

Asia WGS

AF:

0.212

AC:

738

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

Apr 12, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.6

DANN

Benign

0.75

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