chr10-37894641-A-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF33CP		n.37894641A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF33CP	ENST00000432492.1	n.5A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs7099777; hg19: chr10-38183569;