1-154142229-C-T

Variant names:

• chr1-154142229-C-T
• rs6667928
• NM_207308.3:c.473-705G>A

Variant summary

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

The NM_207308.3(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 NM_207308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 7 publications found

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]

NUP210L Gene-Disease associations (from GenCC):

• spermatogenic failure

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207308.3. 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
	NUP210L	NM_207308.3	MANE Select	c.473-705G>A		intron	N/A	NP_997191.2	Q5VU65-1
	NUP210L	NM_001159484.1		c.473-705G>A		intron	N/A	NP_001152956.1	Q5VU65-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP210L	ENST00000368559.8	TSL:5 MANE Select	c.473-705G>A		intron	N/A	ENSP00000357547.3	Q5VU65-1
	NUP210L	ENST00000271854.3	TSL:5	c.473-705G>A		intron	N/A	ENSP00000271854.3	Q5VU65-2

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

African (AFR) AF: 0.139 AC: 5691 AN: 41030

American (AMR) AF: 0.452 AC: 6849 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2223 AN: 5134

South Asian (SAS) AF: 0.376 AC: 1791 AN: 4768

European-Finnish (FIN) AF: 0.380 AC: 3884 AN: 10216

Middle Eastern (MID) AF: 0.359 AC: 104 AN: 290

European-Non Finnish (NFE) AF: 0.337 AC: 22863 AN: 67772

Other (OTH) AF: 0.343 AC: 719 AN: 2094

Alfa AF: 0.309 Hom.: 1329

Bravo AF: 0.306

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.73
DANN	Benign	0.66
PhyloP100		-1.1
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: rs6667928; hg19: chr1-154114705;