rs4105175

Variant names:

• chr5-179028746-A-C
• rs4105175
• NM_001136116.3:c.256+619A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-179028746-A-C
• chr5-179028746-A-G
• chr5-179028746-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001136116.3(ZNF879):​c.256+619A>C variant causes a intron 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: ZNF879 NM_001136116.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.73
• Publications: 5 publications found

Genes affected

ZNF879 (HGNC:37273): (zinc finger protein 879) This gene encodes a kruppel-associated box-containing zinc finger protein (KRAB-ZFP). The encoded protein contains an N-terminal kruppel-associated box (KRAB) domain and thirteen C-terminal C2H2-type zinc finger domains. The KRAB-ZFPs represent the largest family of mammalian transcriptional repressors, which function through the recruitment of the nuclear co-factor KRAB-Associated Protein 1 (KAP1), to engage histone modifiers and induce heterochromatin formation. [provided by RefSeq, Jul 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136116.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF879	NM_001136116.3	MANE Select	c.256+619A>C		intron	N/A	NP_001129588.1	B4DU55
	ZNF879	NM_001353372.2		c.256+619A>C		intron	N/A	NP_001340301.1	B4DU55
	ZNF879	NM_001353373.2		c.256+619A>C		intron	N/A	NP_001340302.1	B4DU55

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF879	ENST00000444149.7	TSL:1 MANE Select	c.256+619A>C		intron	N/A	ENSP00000414887.2	B4DU55
	ZNF879	ENST00000866182.1		c.256+619A>C		intron	N/A	ENSP00000536241.1
	ZNF879	ENST00000866183.1		c.256+619A>C		intron	N/A	ENSP00000536242.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.27
PhyloP100		-4.7

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

Other links and lift over

dbSNP: rs4105175; hg19: chr5-178455747;