chr16-56798381-T-C

Variant names:

• chr16-56798381-T-C
• rs146228854
• NM_014669.5:c.298-95T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_014669.5(NUP93):​c.298-95T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 983,872 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.012 (45 hom., cov: 32)
  • Exomes 𝑓: 0.0014 (18 hom.)
• Consequence: NUP93 NM_014669.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0320

Genes affected

NUP93 (HGNC:28958): (nucleoporin 93) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. This gene encodes a nucleoporin protein that localizes both to the basket of the pore and to the nuclear entry of the central gated channel of the pore. The encoded protein is a target of caspase cysteine proteases that play a central role in programmed cell death by apoptosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 16-56798381-T-C is Benign according to our data. Variant chr16-56798381-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1215493.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0125 (1900/152316) while in subpopulation AFR AF = 0.0435 (1807/41544). AF 95% confidence interval is 0.0418. There are 45 homozygotes in GnomAd4. There are 922 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP93	NM_014669.5	c.298-95T>C		intron_variant	Intron 3 of 21	ENST00000308159.10	NP_055484.3
NUP93	NM_001242795.2	c.-72-95T>C		intron_variant	Intron 1 of 19		NP_001229724.1
NUP93	NM_001242796.2	c.-72-95T>C		intron_variant	Intron 1 of 19		NP_001229725.1
NUP93	XM_005256263.4	c.298-95T>C		intron_variant	Intron 3 of 21		XP_005256320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP93	ENST00000308159.10	c.298-95T>C		intron_variant	Intron 3 of 21	1	NM_014669.5	ENSP00000310668.5

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1886 AN: 152198 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00451

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00813

GnomAD4 exome AF: 0.00140 AC: 1165 AN: 831556 Hom.: 18 AF XY: 0.00115 AC XY: 498 AN XY: 433330

Gnomad4 AFR exome AF: 0.0425 AC: 866 AN: 20382

Gnomad4 AMR exome AF: 0.00250 AC: 91 AN: 36396

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 20722

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 34074

Gnomad4 SAS exome AF: 0.000119 AC: 8 AN: 67372

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 50458

Gnomad4 NFE exome AF: 0.000106 AC: 59 AN: 558386

Gnomad4 Remaining exome AF: 0.00351 AC: 138 AN: 39282

GnomAD4 genome AF: 0.0125 AC: 1900 AN: 152316 Hom.: 45 Cov.: 32 AF XY: 0.0124 AC XY: 922 AN XY: 74500

Gnomad4 AFR AF: 0.0435 AC: 0.0434961 AN: 0.0434961

Gnomad4 AMR AF: 0.00451 AC: 0.00450627 AN: 0.00450627

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000207 AC: 0.000207125 AN: 0.000207125

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000735 AC: 0.0000734991 AN: 0.0000734991

Gnomad4 OTH AF: 0.00804 AC: 0.00804163 AN: 0.00804163

Alfa AF: 0.0101 Hom.: 3

Bravo AF: 0.0141

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 26, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.51
Mutation Taster		=100/0	polymorphism

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: rs146228854; hg19: chr16-56832293;