rs999647

Variant names:

• chr18-74859594-A-C
• NM_017757.3:c.4878-17603A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-74859594-A-C
• chr18-74859594-A-G
• chr18-74859594-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017757.3(ZNF407):​c.4878-17603A>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: 33)
• Consequence: ZNF407 NM_017757.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

Genes affected

ZNF407 (HGNC:19904): (zinc finger protein 407) This gene encodes a zinc finger protein whose exact function is not known. It may be involved in transcriptional regulation. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF407	NM_017757.3	c.4878-17603A>C		intron_variant	Intron 4 of 8	ENST00000299687.10	NP_060227.2
ZNF407	NM_001384475.1	c.4878-17603A>C		intron_variant	Intron 4 of 8		NP_001371404.1
ZNF407	NM_001146189.1	c.4878-17603A>C		intron_variant	Intron 3 of 6		NP_001139661.1
ZNF407	XM_017025838.3	c.4878-17603A>C		intron_variant	Intron 4 of 7		XP_016881327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF407	ENST00000299687.10	c.4878-17603A>C		intron_variant	Intron 4 of 8	1	NM_017757.3	ENSP00000299687.4
ZNF407	ENST00000577538.5	c.4878-17603A>C		intron_variant	Intron 3 of 6	2		ENSP00000463270.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.016
DANN	Benign	0.44

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-72571550;