19-30490160-CTT-C

Variant names:

• chr19-30490160-CTT-C
• rs3837960
• NM_014717.3:c.2170+44437_2170+44438delTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_014717.3(ZNF536):​c.2170+44437_2170+44438delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF536 NM_014717.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

Genes affected

ZNF536 (HGNC:29025): (zinc finger protein 536) The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014717.3. 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
	ZNF536	NM_014717.3	MANE Select	c.2170+44437_2170+44438delTT		intron	N/A	NP_055532.1	O15090
	ZNF536	NM_001376110.1		c.2170+44437_2170+44438delTT		intron	N/A	NP_001363039.1	K7EQN6
	ZNF536	NM_001376111.1		c.2170+44437_2170+44438delTT		intron	N/A	NP_001363040.1	K7EQN6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	ENST00000355537.4	TSL:1 MANE Select	c.2170+44429_2170+44430delTT		intron	N/A	ENSP00000347730.1	O15090
	ZNF536	ENST00000592773.3	TSL:5	c.2170+44429_2170+44430delTT		intron	N/A	ENSP00000467909.3	K7EQN6
	ZNF536	ENST00000706148.1		c.2170+44429_2170+44430delTT		intron	N/A	ENSP00000516231.1	A0A994J7Z0

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

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.25

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: rs3837960; hg19: chr19-30981067;