rs4924682

Positions:

• chr15-42479102-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366845.3(ZNF106):​c.-32-6781A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,206 control chromosomes in the GnomAD database, including 649 homozygotes. 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: 𝑓 0.062 (649 hom., cov: 32)
• Consequence: ZNF106 NM_001366845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

ZNF106 (HGNC:12886): (zinc finger protein 106) Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF106	NM_001366845.3	c.-32-6781A>G		intron_variant		ENST00000564754.7	NP_001353774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF106	ENST00000564754.7	c.-32-6781A>G		intron_variant		1	NM_001366845.3	ENSP00000456845	P1
ZNF106	ENST00000565380.5	c.-32-6781A>G		intron_variant		1		ENSP00000455674
ZNF106	ENST00000567041.1	c.-32-6781A>G		intron_variant		5		ENSP00000454882

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9427 AN: 152088 Hom.: 643 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0895

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00937

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0621 AC: 9453 AN: 152206 Hom.: 649 Cov.: 32 AF XY: 0.0636 AC XY: 4738 AN XY: 74440

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0889

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00935

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0306 Hom.: 95

Bravo AF: 0.0749

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924682; hg19: chr15-42771300;