17-49368389-G-A

Variant names:

• chr17-49368389-G-A
• rs2411984
• ENST00000510360.6:n.105-1410G>A

Variant summary

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

The ENST00000510360.6(ZNF652-AS1):​n.105-1410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 124,798 control chromosomes in the GnomAD database, including 2,420 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 0.19 (2420 hom., cov: 21)
• Consequence: ZNF652-AS1 ENST00000510360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 24 publications found

Genes affected

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

ENSG00000300094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510360.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652-AS1	NR_110883.1		n.101+4040G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652-AS1	ENST00000510360.6	TSL:5	n.105-1410G>A		intron	N/A
	ZNF652-AS1	ENST00000511322.2	TSL:2	n.129+4040G>A		intron	N/A
	ENSG00000300094	ENST00000768748.1		n.300-3003C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 23665 AN: 124710 Hom.: 2407 Cov.: 21

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.190 AC: 23703 AN: 124798 Hom.: 2420 Cov.: 21 AF XY: 0.190 AC XY: 11501 AN XY: 60524

African (AFR) AF: 0.184 AC: 6328 AN: 34466

American (AMR) AF: 0.221 AC: 2637 AN: 11910

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 473 AN: 2600

East Asian (EAS) AF: 0.219 AC: 962 AN: 4398

South Asian (SAS) AF: 0.290 AC: 1013 AN: 3488

European-Finnish (FIN) AF: 0.153 AC: 1221 AN: 8006

Middle Eastern (MID) AF: 0.229 AC: 49 AN: 214

European-Non Finnish (NFE) AF: 0.183 AC: 10462 AN: 57238

Other (OTH) AF: 0.208 AC: 349 AN: 1676

Alfa AF: 0.509 Hom.: 3625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.36
PhyloP100		-0.17
Mutation Taster		=61/39	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2411984; hg19: chr17-47445751; COSMIC: COSV72245271;