rs1735641

Variant names:

• chr10-37895924-C-A
• rs1735641
• ENST00000432492.1:n.1288C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.53).
• 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 rank	MANE	Protein	UniProt
ZNF33CP		n.37895924C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF33CP	ENST00000432492.1	n.1288C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.746 AC: 1220 AN: 1636

American (AMR) AF: 0.674 AC: 3191 AN: 4736

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 1577 AN: 2046

East Asian (EAS) AF: 0.883 AC: 2143 AN: 2428

South Asian (SAS) AF: 0.911 AC: 17818 AN: 19566

European-Finnish (FIN) AF: 0.839 AC: 8280 AN: 9872

Middle Eastern (MID) AF: 0.776 AC: 593 AN: 764

European-Non Finnish (NFE) AF: 0.766 AC: 47097 AN: 61510

Other (OTH) AF: 0.777 AC: 4072 AN: 5244

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

African (AFR) AF: 0.779 AC: 32336 AN: 41498

American (AMR) AF: 0.720 AC: 10984 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2678 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4626 AN: 5162

South Asian (SAS) AF: 0.927 AC: 4476 AN: 4828

European-Finnish (FIN) AF: 0.838 AC: 8877 AN: 10594

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52037 AN: 67998

Other (OTH) AF: 0.756 AC: 1593 AN: 2108

Alfa AF: 0.768 Hom.: 25852

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1735641; hg19: chr10-38184852;