5-150896085-T-G

Variant names:

• chr5-150896085-T-G
• rs765108536
• NM_052860.4:c.1154A>C

Variant summary

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

The NM_052860.4(ZNF300):​c.1154A>C​(p.Glu385Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF300 NM_052860.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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]

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]

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=0.20316291).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF300	NM_052860.4	c.1154A>C	p.Glu385Ala	missense_variant	Exon 6 of 6	ENST00000274599.10	NP_443092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF300	ENST00000274599.10	c.1154A>C	p.Glu385Ala	missense_variant	Exon 6 of 6	1	NM_052860.4	ENSP00000274599.5
ZNF300	ENST00000446148.7	c.1154A>C	p.Glu385Ala	missense_variant	Exon 7 of 7	1		ENSP00000397178.3
IRGM	ENST00000520549.1	n.*141-4504T>G		intron_variant	Intron 3 of 3	1		ENSP00000429819.1
ZNF300	ENST00000427179	c.*1969A>C		3_prime_UTR_variant	Exon 5 of 5	2		ENSP00000414195.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.17	.;T;.;.
Eigen	Benign	0.069
Eigen_PC	Benign	-0.062
FATHMM_MKL	Benign	0.00029	N
LIST_S2	Benign	0.090	T;T;T;T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.20	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	.;L;.;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Pathogenic	-4.5	D;D;D;D
REVEL	Benign	0.11
Sift	Uncertain	0.0030	D;D;D;D
Sift4G	Uncertain	0.057	T;T;T;D
Polyphen		0.94	.;P;.;.
Vest4		0.20
MutPred		0.49		.;Gain of MoRF binding (P = 0.0567);.;Gain of MoRF binding (P = 0.0567);
MVP		0.32
MPC		0.45
ClinPred		0.91	D
GERP RS		2.3
Varity_R		0.43
gMVP		0.071

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

Other links and lift over

dbSNP: rs765108536; hg19: chr5-150275647;