Variant rs6075337 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001367614.1(DZANK1):c.1485G>C(p.Leu495Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 1,612,512 control chromosomes in the GnomAD database, including 474,713 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.71 ( 39272 hom., cov: 31)

Exomes 𝑓: 0.77 ( 435441 hom. )

Consequence

DZANK1
NM_001367614.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.921

Variant links:

Genes affected

DZANK1 (HGNC:15858): (double zinc ribbon and ankyrin repeat domains 1) This gene contains two ankyrin repeat-encoding regions. Ankyrin repeats are tandemly repeated modules of about 33 amino acids described as L-shaped structures consisting of a beta-hairpin and two alpha-helices. Ankyrin repeats occur in a large number of functionally diverse proteins, mainly from eukaryotes, and are known to function as protein-protein interaction domains. [provided by RefSeq, Dec 2018]

DZANK1 links:

DZANK1 (HGNC:):

DZANK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP7

Synonymous conserved (PhyloP=0.921 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DZANK1	NM_001367614.1 linkuse as main transcript	c.1485G>C	p.Leu495Leu	synonymous_variant	13/21	ENST00000699568.1	NP_001354543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DZANK1	ENST00000699568.1 linkuse as main transcript	c.1485G>C	p.Leu495Leu	synonymous_variant	13/21		NM_001367614.1	ENSP00000514442.1	A0A8V8TNE5
DZANK1	ENST00000699590.1 linkuse as main transcript	c.1443G>C	p.Leu481Leu	synonymous_variant	13/21			ENSP00000514461.1	A0A8V8TPU7
DZANK1	ENST00000699525.1 linkuse as main transcript	c.1428G>C	p.Leu476Leu	synonymous_variant	13/21			ENSP00000514418.1	A0A8V8TNH6
DZANK1	ENST00000357236.8 linkuse as main transcript	c.831G>C	p.Leu277Leu	synonymous_variant	9/17	5		ENSP00000349774.5	A0A0A0MRE2
DZANK1	ENST00000480488.2 linkuse as main transcript	c.24G>C	p.Leu8Leu	synonymous_variant	2/6	5		ENSP00000484666.1	A0A087X236
DZANK1	ENST00000377630.9 linkuse as main transcript	n.*616G>C		non_coding_transcript_exon_variant	12/20	2		ENSP00000366857.6	A0A087WTH2
DZANK1	ENST00000460891.5 linkuse as main transcript	n.*1873G>C		non_coding_transcript_exon_variant	13/14	2		ENSP00000477872.1	A0A087WTH2
DZANK1	ENST00000377630.9 linkuse as main transcript	n.*616G>C		3_prime_UTR_variant	12/20	2		ENSP00000366857.6	A0A087WTH2
DZANK1	ENST00000460891.5 linkuse as main transcript	n.*1873G>C		3_prime_UTR_variant	13/14	2		ENSP00000477872.1	A0A087WTH2

Frequencies

GnomAD3 genomes

AF:

0.711

AC:

107991

AN:

151890

Hom.:

39250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.763

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.736

Gnomad NFE

AF:

0.784

Gnomad OTH

AF:

0.728

GnomAD3 exomes

AF:

0.707

AC:

176076

AN:

248968

Hom.:

64999

AF XY:

0.724

AC XY:

97818

AN XY:

135068

show subpopulations

Gnomad AFR exome

AF:

0.638

Gnomad AMR exome

AF:

0.550

Gnomad ASJ exome

AF:

0.778

Gnomad EAS exome

AF:

0.287

Gnomad SAS exome

AF:

0.829

Gnomad FIN exome

AF:

0.754

Gnomad NFE exome

AF:

0.782

Gnomad OTH exome

AF:

0.736

GnomAD4 exome

AF:

0.767

AC:

1119670

AN:

1460502

Hom.:

435441

Cov.:

AF XY:

0.770

AC XY:

559346

AN XY:

726554

show subpopulations

Gnomad4 AFR exome

AF:

0.639

Gnomad4 AMR exome

AF:

0.563

Gnomad4 ASJ exome

AF:

0.776

Gnomad4 EAS exome

AF:

0.334

Gnomad4 SAS exome

AF:

0.828

Gnomad4 FIN exome

AF:

0.752

Gnomad4 NFE exome

AF:

0.791

Gnomad4 OTH exome

AF:

0.748

GnomAD4 genome

AF:

0.711

AC:

108056

AN:

152010

Hom.:

39272

Cov.:

AF XY:

0.707

AC XY:

52529

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.641

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.763

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.807

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.784

Gnomad4 OTH

AF:

0.729

Alfa

AF:

0.766

Hom.:

14539

Bravo

AF:

0.694

Asia WGS

AF:

0.570

AC:

1986

AN:

3478

EpiCase

AF:

0.785

EpiControl

AF:

0.782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

4.2

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over