19-52967183-C-T

Variant names:

• chr19-52967183-C-T
• rs9967593
• ENST00000651287.1:n.4462G>A

Variant summary

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

The ENST00000651287.1(ZNF702P):​n.4462G>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 0.0804 in 152,172 control chromosomes in the GnomAD database, including 571 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 0.080 (571 hom., cov: 31)
• Consequence: ZNF702P ENST00000651287.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

ZNF702P (HGNC:25775): (zinc finger protein 702, pseudogene) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000269082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF702P	ENST00000651287.1	n.4462G>A		non_coding_transcript_exon_variant	Exon 7 of 7
ZNF702P	ENST00000652240.1	n.4198G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000269082	ENST00000600068.1	n.489+3441G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0803 AC: 12208 AN: 152054 Hom.: 567 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0277

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0853

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0804 AC: 12231 AN: 152172 Hom.: 571 Cov.: 31 AF XY: 0.0779 AC XY: 5793 AN XY: 74370

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.00657

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.0709 Hom.: 209

Bravo AF: 0.0830

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9967593; hg19: chr19-53470436;