Variant rs1390364679 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001393494.1(IL34):c.646C>A(p.Pro216Thr) 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

IL34
NM_001393494.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Variant links:

Genes affected

IL34 (HGNC:28529): (interleukin 34) Interleukin-34 is a cytokine that promotes the differentiation and viability of monocytes and macrophages through the colony-stimulating factor-1 receptor (CSF1R; MIM 164770) (Lin et al., 2008 [PubMed 18467591]).[supplied by OMIM, May 2008]

IL34 links:

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ACMG classification

Classification made for transcript

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=0.13382334).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL34	NM_001393494.1 link	c.646C>A	p.Pro216Thr	missense_variant	Exon 6 of 6	ENST00000288098.7	NP_001380423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL34	ENST00000288098.7 link	c.646C>A	p.Pro216Thr	missense_variant	Exon 6 of 6	1	NM_001393494.1	ENSP00000288098.2	Q6ZMJ4-1
IL34	ENST00000566361.1 link	c.571C>A	p.Pro191Thr	missense_variant	Exon 6 of 6	1		ENSP00000463886.1	J3QQT3
IL34	ENST00000429149.6 link	c.646C>A	p.Pro216Thr	missense_variant	Exon 7 of 7	5		ENSP00000397863.2	Q6ZMJ4-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

6.7

DANN

Uncertain

0.98

DEOGEN2

Benign

0.013

T;T;T

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.091

LIST_S2

Benign

0.48

T;.;T

M_CAP

Benign

0.027

MetaRNN

Benign

0.13

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

L;L;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.94

N;N;.

REVEL

Benign

0.037

Sift

Uncertain

0.014

D;D;.

Sift4G

Benign

0.072

T;T;T

Polyphen

0.57

P;P;.

Vest4

0.16

MutPred

0.16

Gain of phosphorylation at P216 (P = 0.044);Gain of phosphorylation at P216 (P = 0.044);.;

MVP

0.26

MPC

0.045

ClinPred

0.16

GERP RS

-2.2

Varity_R

0.044

gMVP

0.23

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