rs6136363

Variant names:

• chr20-18406000-A-G
• rs6136363
• NM_001367614.1:c.1507+6646T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367614.1(DZANK1):​c.1507+6646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,142 control chromosomes in the GnomAD database, including 11,193 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 0.37 (11193 hom., cov: 33)
• Consequence: DZANK1 NM_001367614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DZANK1	NM_001367614.1	c.1507+6646T>C		intron_variant	Intron 13 of 20	ENST00000699568.1	NP_001354543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DZANK1	ENST00000699568.1	c.1507+6646T>C		intron_variant	Intron 13 of 20		NM_001367614.1	ENSP00000514442.1
DZANK1	ENST00000699590.1	c.1465+6646T>C		intron_variant	Intron 13 of 20			ENSP00000514461.1
DZANK1	ENST00000699525.1	c.1450+6646T>C		intron_variant	Intron 13 of 20			ENSP00000514418.1
DZANK1	ENST00000357236.8	c.853+6646T>C		intron_variant	Intron 9 of 16	5		ENSP00000349774.5
DZANK1	ENST00000480488.2	c.46+6646T>C		intron_variant	Intron 2 of 5	5		ENSP00000484666.1
DZANK1	ENST00000377630.9	n.*638+6646T>C		intron_variant	Intron 12 of 19	2		ENSP00000366857.6
DZANK1	ENST00000460891.5	n.*1895+6646T>C		intron_variant	Intron 13 of 13	2		ENSP00000477872.1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 56018 AN: 152024 Hom.: 11182 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.388

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.368 AC: 56036 AN: 152142 Hom.: 11193 Cov.: 33 AF XY: 0.366 AC XY: 27199 AN XY: 74364

African (AFR) AF: 0.244 AC: 10115 AN: 41506

American (AMR) AF: 0.327 AC: 4993 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3468

East Asian (EAS) AF: 0.128 AC: 663 AN: 5168

South Asian (SAS) AF: 0.403 AC: 1947 AN: 4834

European-Finnish (FIN) AF: 0.439 AC: 4641 AN: 10580

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30748 AN: 67986

Other (OTH) AF: 0.386 AC: 814 AN: 2110

Alfa AF: 0.417 Hom.: 16957

Bravo AF: 0.349

Asia WGS AF: 0.267 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.65
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6136363; hg19: chr20-18386644;