rs1735641

Positions:

• chr10-37895924-C-A
• chr10-37895924-C-G
• chr10-37895924-C-T

Variant summary

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

The ENST00000432492.1(ZNF33CP):​n.1288C>A 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 0.787 in 259,930 control chromosomes in the GnomAD database, including 80,901 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 0.78 (46299 hom., cov: 32)
  • Exomes 𝑓: 0.80 (34602 hom.)
• Consequence: ZNF33CP ENST00000432492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.904 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.1288C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118385 AN: 152010 Hom.: 46253 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.798 AC: 85991 AN: 107802 Hom.: 34602 Cov.: 0 AF XY: 0.809 AC XY: 47899 AN XY: 59204

Gnomad4 AFR exome AF: 0.746

Gnomad4 AMR exome AF: 0.674

Gnomad4 ASJ exome AF: 0.771

Gnomad4 EAS exome AF: 0.883

Gnomad4 SAS exome AF: 0.911

Gnomad4 FIN exome AF: 0.839

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.777

GnomAD4 genome AF: 0.779 AC: 118485 AN: 152128 Hom.: 46299 Cov.: 32 AF XY: 0.783 AC XY: 58234 AN XY: 74378

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.756

Alfa AF: 0.769 Hom.: 15076

Bravo AF: 0.765

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.77
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1735641; hg19: chr10-38184852;