Variant chr1-113905292-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000650596.1(DCLRE1B):c.-295G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 406,054 control chromosomes in the GnomAD database, including 29,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 15496 hom., cov: 33)

Exomes 𝑓: 0.31 ( 13763 hom. )

Consequence

DCLRE1B
ENST00000650596.1 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.08

Variant links:

Genes affected

DCLRE1B (HGNC:17641): (DNA cross-link repair 1B) DNA interstrand cross-links prevent strand separation, thereby physically blocking transcription, replication, and segregation of DNA. DCLRE1B is one of several evolutionarily conserved genes involved in repair of interstrand cross-links (Dronkert et al., 2000 [PubMed 10848582]).[supplied by OMIM, Mar 2008]

DCLRE1B links:

AP4B1 (HGNC:572): (adaptor related protein complex 4 subunit beta 1) This gene encodes a subunit of a heterotetrameric adapter-like complex 4 that is involved in targeting proteins from the trans-Golgi network to the endosomal-lysosomal system. Mutations in this gene are associated with cerebral palsy spastic quadriplegic type 5 (CPSQ5) disorder. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

AP4B1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 1-113905292-G-T is Benign according to our data. Variant chr1-113905292-G-T is described in ClinVar as [Benign]. Clinvar id is 1259443.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCLRE1B	NM_022836.4 linkuse as main transcript			upstream_gene_variant		ENST00000650450.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCLRE1B	ENST00000650450.2 linkuse as main transcript			upstream_gene_variant			NM_022836.4	P1

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61852

AN:

151910

Hom.:

15466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.705

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.0756

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.378

GnomAD4 exome

AF:

0.310

AC:

78818

AN:

254026

Hom.:

13763

Cov.:

AF XY:

0.309

AC XY:

40941

AN XY:

132406

show subpopulations

Gnomad4 AFR exome

AF:

0.707

Gnomad4 AMR exome

AF:

0.213

Gnomad4 ASJ exome

AF:

0.407

Gnomad4 EAS exome

AF:

0.0965

Gnomad4 SAS exome

AF:

0.321

Gnomad4 FIN exome

AF:

0.265

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.335

GnomAD4 genome

AF:

0.407

AC:

61932

AN:

152028

Hom.:

15496

Cov.:

AF XY:

0.399

AC XY:

29642

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.705

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.0757

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.345

Hom.:

5675

Bravo

AF:

0.414

Asia WGS

AF:

0.214

AC:

746

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.90

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