17-49374901-C-T

Variant names:

• chr17-49374901-C-T
• rs11655191
• ENST00000511322.2:n.272-409C>T

Variant summary

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

The ENST00000511322.2(ZNF652-AS1):​n.272-409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 122,764 control chromosomes in the GnomAD database, including 314 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 0.066 (314 hom., cov: 22)
• Consequence: ZNF652-AS1 ENST00000511322.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0916 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_110883.1		n.244-409C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF652-AS1	ENST00000511322.2	TSL:2	n.272-409C>T		intron	N/A
	ZNF652-AS1	ENST00000576461.1	TSL:5	n.270+1815C>T		intron	N/A
	ENSG00000300094	ENST00000768748.1		n.299+2299G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 8099 AN: 122746 Hom.: 314 Cov.: 22

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0289

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000238

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0659 AC: 8094 AN: 122764 Hom.: 314 Cov.: 22 AF XY: 0.0646 AC XY: 3682 AN XY: 56982

African (AFR) AF: 0.0350 AC: 1068 AN: 30540

American (AMR) AF: 0.0805 AC: 779 AN: 9680

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 504 AN: 3344

East Asian (EAS) AF: 0.000239 AC: 1 AN: 4192

South Asian (SAS) AF: 0.0997 AC: 395 AN: 3962

European-Finnish (FIN) AF: 0.0342 AC: 171 AN: 4998

Middle Eastern (MID) AF: 0.207 AC: 34 AN: 164

European-Non Finnish (NFE) AF: 0.0788 AC: 4997 AN: 63406

Other (OTH) AF: 0.0744 AC: 120 AN: 1612

Alfa AF: 0.0620 Hom.: 46

Bravo AF: 0.0578

Asia WGS AF: 0.0390 AC: 136 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.46
PhyloP100		-1.6

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: rs11655191;

hg19: chr17-47452263;