Variant rs17800771 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_052860.4(ZNF300):c.1014G>A(p.Ser338Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 1,613,318 control chromosomes in the GnomAD database, including 2,102 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 0.044 ( 199 hom., cov: 32)

Exomes 𝑓: 0.045 ( 1903 hom. )

Consequence

ZNF300
NM_052860.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.57

Variant links:

Genes affected

ZNF300 (HGNC:13091): (zinc finger protein 300) The protein encoded by this gene is a C2H2-type zinc finger DNA binding protein and likely transcriptional regulator. The function of this protein is not yet known. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

ZNF300 links:

IRGM (HGNC:29597): (immunity related GTPase M) This gene encodes a member of the p47 immunity-related GTPase family. The encoded protein may play a role in the innate immune response by regulating autophagy formation in response to intracellular pathogens. Polymorphisms that affect the normal expression of this gene are associated with a susceptibility to Crohn's disease and tuberculosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]

IRGM links:

IRGM (HGNC:):

IRGM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP7

Synonymous conserved (PhyloP=-3.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF300	NM_052860.4 linkuse as main transcript	c.1014G>A	p.Ser338Ser	synonymous_variant	6/6	ENST00000274599.10	NP_443092.1	Q96RE9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZNF300	ENST00000274599.10 linkuse as main transcript	c.1014G>A	p.Ser338Ser	synonymous_variant	6/6	1	NM_052860.4	ENSP00000274599.5	Q96RE9-1
ZNF300	ENST00000446148.7 linkuse as main transcript	c.1014G>A	p.Ser338Ser	synonymous_variant	7/7	1		ENSP00000397178.3	Q96RE9-3
IRGM	ENST00000520549.1 linkuse as main transcript	n.*141-4364C>T		intron_variant		1		ENSP00000429819.1	A0A9H4B933
ZNF300	ENST00000427179.5 linkuse as main transcript	c.*1829G>A		3_prime_UTR_variant	5/5	2		ENSP00000414195.1	F8WE31

Frequencies

GnomAD3 genomes

AF:

0.0443

AC:

6730

AN:

151830

Hom.:

200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0360

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.0627

Gnomad FIN

AF:

0.0328

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.0428

Gnomad OTH

AF:

0.0388

GnomAD3 exomes

AF:

0.0493

AC:

12317

AN:

250066

Hom.:

465

AF XY:

0.0505

AC XY:

6839

AN XY:

135466

show subpopulations

Gnomad AFR exome

AF:

0.0355

Gnomad AMR exome

AF:

0.0184

Gnomad ASJ exome

AF:

0.0380

Gnomad EAS exome

AF:

0.166

Gnomad SAS exome

AF:

0.0625

Gnomad FIN exome

AF:

0.0309

Gnomad NFE exome

AF:

0.0428

Gnomad OTH exome

AF:

0.0434

GnomAD4 exome

AF:

0.0453

AC:

66140

AN:

1461370

Hom.:

1903

Cov.:

AF XY:

0.0458

AC XY:

33330

AN XY:

726968

show subpopulations

Gnomad4 AFR exome

AF:

0.0394

Gnomad4 AMR exome

AF:

0.0200

Gnomad4 ASJ exome

AF:

0.0398

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.0618

Gnomad4 FIN exome

AF:

0.0293

Gnomad4 NFE exome

AF:

0.0421

Gnomad4 OTH exome

AF:

0.0471

GnomAD4 genome

AF:

0.0443

AC:

6728

AN:

151948

Hom.:

199

Cov.:

AF XY:

0.0451

AC XY:

3352

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.0361

Gnomad4 AMR

AF:

0.0328

Gnomad4 ASJ

AF:

0.0372

Gnomad4 EAS

AF:

0.161

Gnomad4 SAS

AF:

0.0628

Gnomad4 FIN

AF:

0.0328

Gnomad4 NFE

AF:

0.0428

Gnomad4 OTH

AF:

0.0379

Alfa

AF:

0.0427

Hom.:

Bravo

AF:

0.0459

Asia WGS

AF:

0.0810

AC:

280

AN:

3478

EpiCase

AF:

0.0446

EpiControl

AF:

0.0429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.83

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over