rs9967593

Positions:

• chr19-52967183-C-T

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:):

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/exons	MANE	Protein	UniProt
		n.52967183C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF702P	ENST00000651287.1	n.4462G>A		non_coding_transcript_exon_variant	7/7
ZNF702P	ENST00000652240.1	n.4198G>A		non_coding_transcript_exon_variant	3/3
ENSG00000269082	ENST00000600068.1	n.489+3441G>A		intron_variant		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;