rs7099777

Positions:

• chr10-37894641-A-C

Variant summary

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

The ENST00000432492.1(ZNF33CP):​n.5A>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 0.526 in 152,046 control chromosomes in the GnomAD database, including 21,321 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 0.53 (21321 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZNF33CP ENST00000432492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 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.5A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79888 AN: 151928 Hom.: 21314 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.511

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.526 AC: 79914 AN: 152046 Hom.: 21321 Cov.: 32 AF XY: 0.533 AC XY: 39598 AN XY: 74314

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.511

Alfa AF: 0.536 Hom.: 11268

Bravo AF: 0.502

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7099777; hg19: chr10-38183569;