chr17-49363104-A-G

Position:

• chr17-49363104-A-G

Variant summary

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

The ENST00000502823.6(ZNF652-AS1):​n.73-1175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,978 control chromosomes in the GnomAD database, including 10,253 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 0.36 (10253 hom., cov: 31)
• Consequence: ZNF652-AS1 ENST00000502823.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

ZNF652-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF652-AS1	NR_110882.1	n.136+587A>G		intron_variant
ZNF652-AS1	NR_110883.1	n.31-1175A>G		intron_variant
ZNF652-AS1	NR_110884.1	n.58-1175A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF652-AS1	ENST00000502823.6	n.73-1175A>G		intron_variant		4
ZNF652-AS1	ENST00000507337.2	n.136+587A>G		intron_variant		4
ZNF652-AS1	ENST00000510360.6	n.34-1175A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54720 AN: 151860 Hom.: 10245 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.360 AC: 54744 AN: 151978 Hom.: 10253 Cov.: 31 AF XY: 0.354 AC XY: 26312 AN XY: 74280

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.339

Alfa AF: 0.368 Hom.: 19671

Bravo AF: 0.353

Asia WGS AF: 0.174 AC: 608 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	11
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16948048; hg19: chr17-47440466;