1-203798607-AC-CG

Variant names:

• chr1-203798607-AC-CG
• NM_001395895.1:c.1085_1086delACinsCG
• ZBED6 p.Asp362Ala

Variant summary

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

The NM_001395895.1(ZBED6):​c.1085_1086delACinsCG​(p.Asp362Ala) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D362V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZBED6 NM_001395895.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.33
• Publications: 0 publications found

Genes affected

ZBED6 (HGNC:33273): (zinc finger BED-type containing 6) The protein encoded by this transposon-derived intronless gene is a transcriptional repressor that binds to the consensus sequence 5'-GCTCGC-3'. The encoded protein has been shown to repress IGF2 transcription. This gene is located within the first intron of the ZC3H11A gene. [provided by RefSeq, Jul 2016]

ZC3H11A (HGNC:29093): (zinc finger CCCH-type containing 11A) Enables RNA binding activity. Involved in poly(A)+ mRNA export from nucleus. Colocalizes with transcription export complex. [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_001395895.1. 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
	ZBED6	NM_001395895.1	MANE Select	c.1085_1086delACinsCG	p.Asp362Ala	missense	N/A	NP_001382824.1	P86452
	ZC3H11A	NM_001376342.1	MANE Select	c.-1588+2813_-1588+2814delACinsCG		intron	N/A	NP_001363271.1	O75152
	ZBED6	NM_001174108.2		c.1085_1086delACinsCG	p.Asp362Ala	missense	N/A	NP_001167579.1	P86452

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBED6	ENST00000550078.3	TSL:1 MANE Select	c.1085_1086delACinsCG	p.Asp362Ala	missense	N/A	ENSP00000447879.1	P86452
	ZC3H11A	ENST00000367210.3	TSL:1 MANE Select	c.-1588+2813_-1588+2814delACinsCG		intron	N/A	ENSP00000356179.1	O75152
	ZC3H11A	ENST00000332127.8	TSL:1	c.-565+2111_-565+2112delACinsCG		intron	N/A	ENSP00000333253.4	O75152

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		3.3

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: chr1-203767735;