rs7246739

Variant names:

• chr19-37040829-G-A
• rs7246739
• ENST00000587029.5:c.-125+32747G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-37040829-G-A
• chr19-37040829-G-C

Variant summary

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

The ENST00000587029.5(ZNF420):​c.-125+32747G>A 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: 31)
• Consequence: ZNF420 ENST00000587029.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 2 publications found

Genes affected

ZNF420 (HGNC:20649): (zinc finger protein 420) The protein encoded by this gene is a KRAB-type zinc finger protein that negatively-regulates p53-mediated apoptosis. Under stress conditions, the encoded protein is phosphorylated by ATM and dissociates from p53, which activates p53 and initiates apoptosis. [provided by RefSeq, Jul 2016]

ENSG00000300522 (HGNC:):

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=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF420	XM_011526503.3	c.-125+32747G>A		intron_variant	Intron 1 of 4		XP_011524805.1
ZNF420	XM_047438230.1	c.-158+32747G>A		intron_variant	Intron 1 of 5		XP_047294186.1
ZNF420	XM_011526510.3	c.-122+32747G>A		intron_variant	Intron 1 of 2		XP_011524812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF420	ENST00000587029.5	c.-125+32747G>A		intron_variant	Intron 1 of 4	4		ENSP00000466057.1
ZNF420	ENST00000590332.1	c.-78+32747G>A		intron_variant	Intron 1 of 1	4		ENSP00000468387.1
ENSG00000300522	ENST00000772564.1	n.222-20217G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.1
DANN	Benign	0.85
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs7246739; hg19: chr19-37531731;