20-18384553-C-G

Variant names:

• chr20-18384553-C-G
• NM_001367614.1:c.2180G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001367614.1(DZANK1):​c.2180G>C​(p.Ser727Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,450,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S727N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: DZANK1 NM_001367614.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16365919).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DZANK1	NM_001367614.1	c.2180G>C	p.Ser727Thr	missense_variant	Exon 21 of 21	ENST00000699568.1	NP_001354543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DZANK1	ENST00000699568.1	c.2180G>C	p.Ser727Thr	missense_variant	Exon 21 of 21		NM_001367614.1	ENSP00000514442.1
DZANK1	ENST00000699590.1	c.2138G>C	p.Ser713Thr	missense_variant	Exon 21 of 21			ENSP00000514461.1
DZANK1	ENST00000699525.1	c.2123G>C	p.Ser708Thr	missense_variant	Exon 21 of 21			ENSP00000514418.1
DZANK1	ENST00000357236.8	c.1526G>C	p.Ser509Thr	missense_variant	Exon 17 of 17	5		ENSP00000349774.5
DZANK1	ENST00000377630.9	n.*1311G>C		non_coding_transcript_exon_variant	Exon 20 of 20	2		ENSP00000366857.6
DZANK1	ENST00000377630.9	n.*1311G>C		3_prime_UTR_variant	Exon 20 of 20	2		ENSP00000366857.6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1450926 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 720756

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	19
DANN	Benign	0.97
DEOGEN2	Benign	0.0075	T;T;T;.
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.37	N
LIST_S2	Benign	0.80	T;T;.;T
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Benign	-0.56	T
MutationAssessor	Benign	2.0	M;.;M;.
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-1.7	N;.;.;.
REVEL	Benign	0.14
Sift	Benign	0.037	D;.;.;.
Sift4G	Uncertain	0.019	D;D;D;D
Polyphen		0.92	P;.;P;.
Vest4		0.15
MutPred		0.50		Gain of methylation at K706 (P = 0.1121);.;Gain of methylation at K706 (P = 0.1121);.;
MVP		0.25
MPC		0.084
ClinPred		0.61	D
GERP RS		1.4
Varity_R		0.071
gMVP		0.19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-18365197;