rs2722650

Variant names:

• chr19-44397361-G-A
• rs2722650
• NM_152354.6:c.-43-105C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152354.6(ZNF285):​c.-43-105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,328,392 control chromosomes in the GnomAD database, including 47,227 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 0.33 (11737 hom., cov: 31)
  • Exomes 𝑓: 0.20 (35490 hom.)
• Consequence: ZNF285 NM_152354.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 3 publications found

Genes affected

ZNF285 (HGNC:13079): (zinc finger protein 285) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific 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 active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267173 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.038).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152354.6. 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
	ZNF285	NM_152354.6	MANE Select	c.-43-105C>T		intron	N/A	NP_689567.4
	ZNF285	NM_001291488.2		c.-43-105C>T		intron	N/A	NP_001278417.1
	ZNF285	NM_001291489.2		c.-43-105C>T		intron	N/A	NP_001278418.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF285	ENST00000614994.5	TSL:1 MANE Select	c.-43-105C>T		intron	N/A	ENSP00000483662.1
	ENSG00000267173	ENST00000588212.1	TSL:2	c.-43-105C>T		intron	N/A	ENSP00000468271.1
	ZNF285	ENST00000591679.5	TSL:4	c.-43-105C>T		intron	N/A	ENSP00000464788.1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49959 AN: 151700 Hom.: 11689 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.200 AC: 234826 AN: 1176574 Hom.: 35490 AF XY: 0.201 AC XY: 119482 AN XY: 595088

African (AFR) AF: 0.623 AC: 17097 AN: 27428

American (AMR) AF: 0.414 AC: 16350 AN: 39456

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 6103 AN: 23574

East Asian (EAS) AF: 0.752 AC: 28319 AN: 37654

South Asian (SAS) AF: 0.291 AC: 22456 AN: 77178

European-Finnish (FIN) AF: 0.207 AC: 10674 AN: 51582

Middle Eastern (MID) AF: 0.290 AC: 1358 AN: 4686

European-Non Finnish (NFE) AF: 0.139 AC: 119855 AN: 864428

Other (OTH) AF: 0.249 AC: 12614 AN: 50588

GnomAD4 genome AF: 0.330 AC: 50072 AN: 151818 Hom.: 11737 Cov.: 31 AF XY: 0.335 AC XY: 24871 AN XY: 74206

African (AFR) AF: 0.604 AC: 24953 AN: 41284

American (AMR) AF: 0.386 AC: 5891 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3877 AN: 5160

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4814

European-Finnish (FIN) AF: 0.202 AC: 2134 AN: 10566

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 10016 AN: 67944

Other (OTH) AF: 0.325 AC: 684 AN: 2104

Alfa AF: 0.216 Hom.: 18938

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.0
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2722650;