1-154142229-C-T

Variant summary

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

The ENST00000368559.8(NUP210L):c.473-705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 150,822 control chromosomes in the GnomAD database, including 7,860 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 0.30 (7860 hom., cov: 30)
• Consequence: NUP210L ENST00000368559.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

NUP210L (HGNC:29915): (nucleoporin 210 like) Predicted to act upstream of or within Sertoli cell development and spermatid development. Predicted to be integral component of membrane. Predicted to be part of nuclear pore. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUP210L	NM_207308.3	c.473-705G>A		intron_variant		ENST00000368559.8
NUP210L	XM_011510122.2	c.341-705G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUP210L	ENST00000368559.8	c.473-705G>A		intron_variant		5	NM_207308.3	P2
NUP210L	ENST00000271854.3	c.473-705G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 45789 AN: 150728 Hom.: 7855 Cov.: 30

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.304 AC: 45810 AN: 150822 Hom.: 7860 Cov.: 30 AF XY: 0.311 AC XY: 22857 AN XY: 73562

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.343

Alfa AF: 0.313 Hom.: 1314

Bravo AF: 0.306

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.73
Dann	Benign	0.66

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: rs6667928; hg19: chr1-154114705;