rs2738222

chr10-37894746-A-Cchr10-37894746-A-Gchr10-37894746-A-T

Variant summary

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

The ENST00000432492.1(ZNF33CP):n.110A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,224 control chromosomes in the GnomAD database, including 59,461 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 0.88 (59461 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ZNF33CP ENST00000432492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

ZNF33CP (HGNC:30957): (zinc finger protein 33C, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF33CP	ENST00000432492.1	n.110A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134246 AN: 152104 Hom.: 59404 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.864

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.883 AC: 134361 AN: 152222 Hom.: 59461 Cov.: 32 AF XY: 0.882 AC XY: 65679 AN XY: 74428

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.865

Alfa AF: 0.869 Hom.: 11660

Bravo AF: 0.874

Asia WGS AF: 0.916 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738222; hg19: chr10-38183674;