22-22507676-A-G

Variant names:

• chr22-22507676-A-G
• rs361901
• NM_080764.4:c.-187+134T>C

Variant summary

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

The NM_080764.4(ZNF280B):​c.-187+134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,660 control chromosomes in the GnomAD database, including 1,959 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 0.15 (1959 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF280B NM_080764.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 publications found

Genes affected

ZNF280B (HGNC:23022): (zinc finger protein 280B) The protein encoded by this gene is a transcription factor that upregulates expression of MDM2, which negatively regulates p53 expression. This gene is highly expressed in prostate cancer cells, which leads to a reduction in p53 levels and an increase in growth of the cancer cells. Several transcript variants have been found for this gene, but only one of them is protein-coding. [provided by RefSeq, Jan 2015]

IGL (HGNC:5853):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=0.977).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080764.4. 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
	ZNF280B	NM_080764.4	MANE Select	c.-187+134T>C		intron	N/A	NP_542942.2	Q86YH2
	ZNF280B	NR_130642.2		n.145+134T>C		intron	N/A
	ZNF280B	NR_130643.2		n.84+983T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF280B	ENST00000626650.3	TSL:2 MANE Select	c.-187+134T>C		intron	N/A	ENSP00000485750.1	Q86YH2
	ZNF280B	ENST00000619852.2	TSL:1	n.-187+134T>C		intron	N/A	ENSP00000480958.1	Q86YH2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22523 AN: 151540 Hom.: 1959 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.140

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.149 AC: 22526 AN: 151660 Hom.: 1959 Cov.: 31 AF XY: 0.152 AC XY: 11284 AN XY: 74090

African (AFR) AF: 0.209 AC: 8640 AN: 41344

American (AMR) AF: 0.120 AC: 1819 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1108 AN: 5052

South Asian (SAS) AF: 0.295 AC: 1408 AN: 4780

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10566

Middle Eastern (MID) AF: 0.147 AC: 42 AN: 286

European-Non Finnish (NFE) AF: 0.104 AC: 7043 AN: 67932

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.122 Hom.: 2931

Bravo AF: 0.150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.98
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs361901;