16-56728533-G-A

Variant names:

• chr16-56728533-G-A
• rs7197684
• ENST00000561663.7:n.506+973C>T

Variant summary

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

The ENST00000561663.7(NUP93-DT):​n.506+973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 108,502 control chromosomes in the GnomAD database, including 8,910 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 0.46 (8910 hom., cov: 30)
• Consequence: NUP93-DT ENST00000561663.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 1 publications found

Genes affected

NUP93-DT (HGNC:55370): (NUP93 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561663.7. 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
	NUP93-DT	NR_184320.1		n.493+973C>T		intron	N/A
	NUP93-DT	NR_184321.1		n.493+973C>T		intron	N/A
	NUP93-DT	NR_184322.1		n.216+1250C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP93-DT	ENST00000561663.7	TSL:3	n.506+973C>T		intron	N/A
	NUP93-DT	ENST00000564560.1	TSL:5	n.463+973C>T		intron	N/A
	NUP93-DT	ENST00000668197.1		n.221+1250C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 49890 AN: 108436 Hom.: 8906 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.460 AC: 49932 AN: 108502 Hom.: 8910 Cov.: 30 AF XY: 0.466 AC XY: 24404 AN XY: 52424

African (AFR) AF: 0.601 AC: 18779 AN: 31238

American (AMR) AF: 0.492 AC: 4822 AN: 9792

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 739 AN: 2350

East Asian (EAS) AF: 0.622 AC: 2387 AN: 3840

South Asian (SAS) AF: 0.552 AC: 1758 AN: 3186

European-Finnish (FIN) AF: 0.368 AC: 2260 AN: 6148

Middle Eastern (MID) AF: 0.457 AC: 85 AN: 186

European-Non Finnish (NFE) AF: 0.367 AC: 18291 AN: 49802

Other (OTH) AF: 0.480 AC: 704 AN: 1466

Alfa AF: 0.285 Hom.: 1495

Bravo AF: 0.344

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.83
PhyloP100		-0.086

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7197684; hg19: chr16-56762445;