chr7-23190935-A-C

Position:

• chr7-23190935-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP42	NM_007342.3	c.445+3789A>C		intron_variant		ENST00000258742.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP42	ENST00000258742.10	c.445+3789A>C		intron_variant		1	NM_007342.3	P1

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

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.0709

Alfa AF: 0.0687 Hom.: 536

Bravo AF: 0.0470

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.75

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: rs10232205; hg19: chr7-23230554;