16-70639049-G-C

Position:

• chr16-70639049-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152456.3(IL34):​c.-400-7499G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,084 control chromosomes in the GnomAD database, including 27,792 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 0.57 (27792 hom., cov: 32)
• Consequence: IL34 NM_152456.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL34	NM_001172772.2	c.-400-7499G>C		intron_variant			NP_001166243.1
IL34	NM_001393493.1	c.-400-7499G>C		intron_variant			NP_001380422.1
IL34	NM_152456.3	c.-400-7499G>C		intron_variant			NP_689669.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL34	ENST00000429149.6	c.-400-7499G>C		intron_variant		5		ENSP00000397863.2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86209 AN: 151966 Hom.: 27740 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.568 AC: 86320 AN: 152084 Hom.: 27792 Cov.: 32 AF XY: 0.561 AC XY: 41723 AN XY: 74348

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.533

Alfa AF: 0.295 Hom.: 635

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.37

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: rs7193968; hg19: chr16-70672952;