NM_001376110.1:c.-73+14434C>G

Variant names:

• chr19-30240104-C-G
• rs2018622
• NM_001376110.1:c.-73+14434C>G

Variant summary

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

The NM_001376110.1(ZNF536):​c.-73+14434C>G 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: ZNF536 NM_001376110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 0 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: 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=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF536	NM_001376110.1	c.-73+14434C>G		intron_variant	Intron 1 of 5		NP_001363039.1
ZNF536	NM_001376111.1	c.-73+11431C>G		intron_variant	Intron 1 of 5		NP_001363040.1
ZNF536	NM_001438953.1	c.-73+12087C>G		intron_variant	Intron 1 of 5		NP_001425882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF536	ENST00000592773.3	c.-73+12087C>G		intron_variant	Intron 1 of 5	5		ENSP00000467909.3
ZNF536	ENST00000706148.1	c.-73+12087C>G		intron_variant	Intron 1 of 6			ENSP00000516231.1
ZNF536	ENST00000706142.1	c.-190+15189C>G		intron_variant	Intron 1 of 6			ENSP00000516226.1

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-0.074

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2018622; hg19: chr19-30731011;