ENST00000563328.5:n.203-23203G>T

Variant names:

• chr16-72722202-G-T
• rs10500569
• ENST00000563328.5:n.203-23203G>T

Variant summary

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

The ENST00000563328.5(ZFHX3-AS1):​n.203-23203G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,096 control chromosomes in the GnomAD database, including 3,628 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 (3628 hom., cov: 32)
• Consequence: ZFHX3-AS1 ENST00000563328.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 9 publications found

Genes affected

ZFHX3-AS1 (HGNC:56033): (ZFHX3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563328.5. 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
	ZFHX3-AS1	NR_171702.1		n.328+8213G>T		intron	N/A
	ZFHX3-AS1	NR_171703.1		n.285+8786G>T		intron	N/A
	ZFHX3-AS1	NR_171704.1		n.285+8786G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFHX3-AS1	ENST00000563328.5	TSL:3	n.203-23203G>T		intron	N/A
	ZFHX3-AS1	ENST00000653037.2		n.290+8786G>T		intron	N/A
	ZFHX3-AS1	ENST00000668995.1		n.338+8213G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29061 AN: 151978 Hom.: 3628 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.191 AC: 29053 AN: 152096 Hom.: 3628 Cov.: 32 AF XY: 0.187 AC XY: 13883 AN XY: 74354

African (AFR) AF: 0.0529 AC: 2197 AN: 41538

American (AMR) AF: 0.167 AC: 2551 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3464

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5182

South Asian (SAS) AF: 0.108 AC: 523 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10552

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19640 AN: 67946

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.243 Hom.: 10437

Bravo AF: 0.181

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10500569; hg19: chr16-72756101;