rs7197684

chr16-56728533-G-Achr16-56728533-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184322.1(NUP93-DT):n.216+1250C>T variant causes a intron, non coding transcript 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 NR_184322.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP93-DT	NR_184322.1	n.216+1250C>T		intron_variant, non_coding_transcript_variant
NUP93-DT	NR_184320.1	n.493+973C>T		intron_variant, non_coding_transcript_variant
NUP93-DT	NR_184321.1	n.493+973C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP93-DT	ENST00000561663.6	n.505+973C>T		intron_variant, non_coding_transcript_variant		3
NUP93-DT	ENST00000564560.1	n.463+973C>T		intron_variant, non_coding_transcript_variant		5
NUP93-DT	ENST00000668197.1	n.221+1250C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.480

Alfa AF: 0.258 Hom.: 1087

Bravo AF: 0.344

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.4
Dann	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs7197684; hg19: chr16-56762445;