Variant chr3-138063081-A-C 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 NM_173543.3(DZIP1L):c.2143-104T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,301,224 control chromosomes in the GnomAD database, including 443,627 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 40413 hom., cov: 31)

Exomes 𝑓: 0.83 ( 403214 hom. )

Consequence

DZIP1L
NM_173543.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.26

Variant links:

Genes affected

DZIP1L (HGNC:26551): (DAZ interacting zinc finger protein 1 like) Predicted to enable metal ion binding activity. Involved in cilium assembly and regulation of protein localization. Located in ciliary basal body. Colocalizes with centriole. Implicated in polycystic kidney disease 5. [provided by Alliance of Genome Resources, Apr 2022]

DZIP1L 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=-0.81).

BP6

Variant 3-138063081-A-C is Benign according to our data. Variant chr3-138063081-A-C is described in ClinVar as [Benign]. Clinvar id is 1236019.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
DZIP1L	NM_173543.3 link	c.2143-104T>G	intron_variant	ENST00000327532.7	NP_775814.2	Q8IYY4-1
DZIP1L	XM_005247198.4 link	c.2227-104T>G	intron_variant		XP_005247255.1
DZIP1L	XM_047447642.1 link	c.2086-104T>G	intron_variant		XP_047303598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DZIP1L	ENST00000327532.7 link	c.2143-104T>G		intron_variant		1	NM_173543.3	ENSP00000332148.2		Q8IYY4-1

Frequencies

GnomAD3 genomes

AF:

0.697

AC:

105841

AN:

151866

Hom.:

40417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.841

Gnomad AMR

AF:

0.777

Gnomad ASJ

AF:

0.881

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.739

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.864

Gnomad OTH

AF:

0.742

GnomAD4 exome

AF:

0.831

AC:

955492

AN:

1149238

Hom.:

403214

AF XY:

0.831

AC XY:

476534

AN XY:

573572

show subpopulations

Gnomad4 AFR exome

AF:

0.346

Gnomad4 AMR exome

AF:

0.720

Gnomad4 ASJ exome

AF:

0.870

Gnomad4 EAS exome

AF:

0.620

Gnomad4 SAS exome

AF:

0.740

Gnomad4 FIN exome

AF:

0.755

Gnomad4 NFE exome

AF:

0.871

Gnomad4 OTH exome

AF:

0.804

GnomAD4 genome

AF:

0.697

AC:

105867

AN:

151986

Hom.:

40413

Cov.:

AF XY:

0.694

AC XY:

51520

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.362

Gnomad4 AMR

AF:

0.777

Gnomad4 ASJ

AF:

0.881

Gnomad4 EAS

AF:

0.642

Gnomad4 SAS

AF:

0.727

Gnomad4 FIN

AF:

0.739

Gnomad4 NFE

AF:

0.864

Gnomad4 OTH

AF:

0.734

Alfa

AF:

0.839

Hom.:

49342

Bravo

AF:

0.682

Asia WGS

AF:

0.633

AC:

2203

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	clinical testing	GeneDx	May 11, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.79

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