rs16948048

Variant names:

• chr17-49363104-A-G
• rs16948048
• ENST00000502823.6:n.73-1175A>G

Variant summary

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

The ENST00000511322.2(ZNF652-AS1):​n.59-1175A>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 ENST00000511322.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 110 publications found

Genes affected

ZNF652-AS1 (HGNC:55582): (ZNF652 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511322.2. 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
	ZNF652-AS1	NR_110882.1		n.136+587A>G		intron	N/A
	ZNF652-AS1	NR_110883.1		n.31-1175A>G		intron	N/A
	ZNF652-AS1	NR_110884.1		n.58-1175A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652-AS1	ENST00000502823.6	TSL:4	n.73-1175A>G		intron	N/A
	ZNF652-AS1	ENST00000507337.2	TSL:4	n.136+587A>G		intron	N/A
	ZNF652-AS1	ENST00000510360.6	TSL:5	n.34-1175A>G		intron	N/A

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

African (AFR) AF: 0.386 AC: 16010 AN: 41436

American (AMR) AF: 0.273 AC: 4172 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5164

South Asian (SAS) AF: 0.163 AC: 786 AN: 4820

European-Finnish (FIN) AF: 0.430 AC: 4536 AN: 10544

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26084 AN: 67950

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.368 Hom.: 45454

Bravo AF: 0.353

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16948048;

hg19: chr17-47440466;