19-56442215-TT-AA

Variant names:

• chr19-56442215-TT-AA
• NM_001321356.2:c.779_780delAAinsTT
• ZNF667 p.Lys260Ile

Variant summary

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

The NM_001321356.2(ZNF667):​c.779_780delAAinsTT​(p.Lys260Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF667 NM_001321356.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 0 publications found

Genes affected

ZNF667 (HGNC:28854): (zinc finger protein 667) Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321356.2. 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
	ZNF667	NM_001321356.2	MANE Select	c.779_780delAAinsTT	p.Lys260Ile	missense	N/A	NP_001308285.1	Q5HYK9
	ZNF667	NM_022103.4		c.779_780delAAinsTT	p.Lys260Ile	missense	N/A	NP_071386.3
	ZNF667	NM_001321355.2		c.608_609delAAinsTT	p.Lys203Ile	missense	N/A	NP_001308284.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF667	ENST00000504904.8	TSL:2 MANE Select	c.779_780delAAinsTT	p.Lys260Ile	missense	N/A	ENSP00000439402.1	Q5HYK9
	ZNF667	ENST00000292069.10	TSL:1	c.779_780delAAinsTT	p.Lys260Ile	missense	N/A	ENSP00000292069.5	Q5HYK9
	ZNF667	ENST00000909113.1		c.779_780delAAinsTT	p.Lys260Ile	missense	N/A	ENSP00000579172.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-56953584;