rs7099777

Variant names:

• chr10-37894641-A-C
• rs7099777
• ENST00000432492.1:n.5A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432492.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF33CP	ENST00000432492.1	TSL:6	n.5A>C		non_coding_transcript_exon	Exon 1 of 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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.489 AC: 20264 AN: 41476

American (AMR) AF: 0.480 AC: 7324 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2297 AN: 5158

South Asian (SAS) AF: 0.707 AC: 3412 AN: 4826

European-Finnish (FIN) AF: 0.681 AC: 7206 AN: 10576

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35711 AN: 67956

Other (OTH) AF: 0.511 AC: 1081 AN: 2114

Alfa AF: 0.535 Hom.: 12425

Bravo AF: 0.502

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7099777;

hg19: chr10-38183569;