chr7-23190935-A-C

Variant names:

• chr7-23190935-A-C
• rs10232205
• NM_007342.3:c.445+3789A>C

Variant summary

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

The NM_007342.3(NUP42):​c.445+3789A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 152,324 control chromosomes in the GnomAD database, including 234 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 0.046 (234 hom., cov: 32)
• Consequence: NUP42 NM_007342.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 6 publications found

Genes affected

NUP42 (HGNC:17010): (nucleoporin 42) Enables nuclear export signal receptor activity. Involved in protein export from nucleus. Located in cytosol and nucleoplasm. Colocalizes with nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007342.3. 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
	NUP42	NM_007342.3	MANE Select	c.445+3789A>C		intron	N/A	NP_031368.1
	NUP42	NM_001370443.1		c.445+3789A>C		intron	N/A	NP_001357372.1
	NUP42	NM_001370444.1		c.445+3789A>C		intron	N/A	NP_001357373.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP42	ENST00000258742.10	TSL:1 MANE Select	c.445+3789A>C		intron	N/A	ENSP00000258742.5
	NUP42	ENST00000928289.1		c.446-2042A>C		intron	N/A	ENSP00000598348.1
	NUP42	ENST00000879313.1		c.446-2042A>C		intron	N/A	ENSP00000549372.1

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7020 AN: 152206 Hom.: 234 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0716

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

GnomAD4 genome AF: 0.0461 AC: 7021 AN: 152324 Hom.: 234 Cov.: 32 AF XY: 0.0433 AC XY: 3222 AN XY: 74476

African (AFR) AF: 0.0117 AC: 486 AN: 41590

American (AMR) AF: 0.0494 AC: 755 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4824

European-Finnish (FIN) AF: 0.0372 AC: 395 AN: 10608

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4631 AN: 68032

Other (OTH) AF: 0.0709 AC: 150 AN: 2116

Alfa AF: 0.0623 Hom.: 739

Bravo AF: 0.0470

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

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: rs10232205; hg19: chr7-23230554;