rs1650966

Variant names:

• chr19-52971207-A-G
• rs1650966
• ENST00000270443.9:n.468-365T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000270443.9(ZNF702P):​n.468-365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,304 control chromosomes in the GnomAD database, including 566 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 0.081 (566 hom., cov: 32)
• Consequence: ZNF702P ENST00000270443.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 3 publications found

Genes affected

ZNF702P (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000270443.9. 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
	ZNF702P	NR_003578.1		n.406-365T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF702P	ENST00000270443.9	TSL:1	n.468-365T>C		intron	N/A
	ZNF702P	ENST00000598752.5	TSL:3	n.105-365T>C		intron	N/A
	ZNF702P	ENST00000599665.6	TSL:4	n.597-365T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12303 AN: 152186 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0287

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0809 AC: 12325 AN: 152304 Hom.: 566 Cov.: 32 AF XY: 0.0786 AC XY: 5852 AN XY: 74476

African (AFR) AF: 0.134 AC: 5548 AN: 41548

American (AMR) AF: 0.0533 AC: 816 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.0212 AC: 110 AN: 5184

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4834

European-Finnish (FIN) AF: 0.0557 AC: 592 AN: 10622

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0673 AC: 4581 AN: 68024

Other (OTH) AF: 0.0865 AC: 183 AN: 2116

Alfa AF: 0.0778 Hom.: 87

Bravo AF: 0.0834

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.15
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1650966; hg19: chr19-53474460;