rs4924682

Variant names:

• chr15-42479102-T-C
• rs4924682
• NM_001366845.3:c.-32-6781A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF106	NM_001366845.3	MANE Select	c.-32-6781A>G		intron	N/A	NP_001353774.1
	ZNF106	NM_001381993.1		c.-32-6781A>G		intron	N/A	NP_001368922.1
	ZNF106	NM_001366846.3		c.-32-6781A>G		intron	N/A	NP_001353775.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF106	ENST00000564754.7	TSL:1 MANE Select	c.-32-6781A>G		intron	N/A	ENSP00000456845.2
	ZNF106	ENST00000565380.5	TSL:1	c.-32-6781A>G		intron	N/A	ENSP00000455674.1
	ZNF106	ENST00000567041.1	TSL:5	c.-32-6781A>G		intron	N/A	ENSP00000454882.1

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

African (AFR) AF: 0.124 AC: 5161 AN: 41526

American (AMR) AF: 0.156 AC: 2382 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5170

South Asian (SAS) AF: 0.0889 AC: 429 AN: 4824

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00935 AC: 636 AN: 68008

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0516 Hom.: 305

Bravo AF: 0.0749

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.55
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4924682; hg19: chr15-42771300;