12-102119753-G-C

Position:

• chr12-102119753-G-C

Variant summary

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

The NM_024057.4(NUP37):​c.-66+297C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,230 control chromosomes in the GnomAD database, including 398 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 0.036 (398 hom., cov: 32)
• Consequence: NUP37 NM_024057.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

Genes affected

NUP37 (HGNC:29929): (nucleoporin 37) Nuclear pore complexes (NPCs) are used for transporting macromolecules between the cytoplasm and the nucleus. NPCs consist of multiple copies of 30 distinct proteins (nucleoporins), which assemble into biochemically-separable subcomplexes. The protein encoded by this gene is part of a subcomplex (Nup107-160) that is required for proper NPC function as well as for normal kinetochore-microtubule interaction and mitosis. [provided by RefSeq, Dec 2015]

NUP37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP37	NM_024057.4	c.-66+297C>G		intron_variant		ENST00000552283.6	NP_076962.2
NUP37	XM_047429530.1	c.-66+297C>G		intron_variant			XP_047285486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP37	ENST00000552283.6	c.-66+297C>G		intron_variant		5	NM_024057.4	ENSP00000448054.1

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5398 AN: 152112 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0355 AC: 5410 AN: 152230 Hom.: 398 Cov.: 32 AF XY: 0.0407 AC XY: 3029 AN XY: 74432

Gnomad4 AFR AF: 0.00628

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0129

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0236 Hom.: 156

Bravo AF: 0.0369

Asia WGS AF: 0.198 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.35

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: rs2292303; hg19: chr12-102513531;