dbSNP rs209238: ZNF280C:p.Gly617Gly (chrX-130215321-T-A) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_017666.5(ZNF280C):c.1851A>T(p.Gly617Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

ZNF280C
NM_017666.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Publications

13 publications found

Variant links:

Genes affected

ZNF280C (HGNC:25955): (zinc finger protein 280C) This gene encodes a member of the zinc finger domain-containing protein family. This family member contains multiple Cys2-His2(C2H2)-type zinc finger domains, the most common type of zinc finger domain that self-folds to form a beta-beta-alpha structure that binds a zinc ion. [provided by RefSeq, Aug 2011]

ZNF280C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=1.39 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017666.5. 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
	ZNF280C	NM_017666.5	MANE Select	c.1851A>T	p.Gly617Gly	synonymous	Exon 15 of 19	NP_060136.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ZNF280C	ENST00000370978.9	TSL:1 MANE Select	c.1851A>T	p.Gly617Gly	synonymous	Exon 15 of 19	ENSP00000360017.4
ZNF280C	ENST00000447817.1	TSL:1	c.1704A>T	p.Gly568Gly	synonymous	Exon 14 of 14	ENSP00000408521.1
ZNF280C	ENST00000930023.1		c.1851A>T	p.Gly617Gly	synonymous	Exon 15 of 20	ENSP00000600082.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1080705

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

350221

African (AFR)

AF:

0.00

AC:

AN:

25539

American (AMR)

AF:

0.00

AC:

AN:

32609

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18914

East Asian (EAS)

AF:

0.00

AC:

AN:

29413

South Asian (SAS)

AF:

0.00

AC:

AN:

50484

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40235

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4076

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

834094

Other (OTH)

AF:

0.00

AC:

AN:

45341

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

4.0

(source)

DANN

Benign

0.72

PhyloP100

1.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over