rs4845597

Positions:

• chr1-154116962-T-C

Variant summary

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

The NM_207308.3(NUP210L):​c.1620+763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,952 control chromosomes in the GnomAD database, including 8,221 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 0.31 (8221 hom., cov: 31)
• Consequence: NUP210L NM_207308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP210L	NM_207308.3	c.1620+763A>G		intron_variant			NP_997191.2
NUP210L	NM_001159484.1	c.1620+763A>G		intron_variant			NP_001152956.1
NUP210L	XM_017002788.3	c.1620+763A>G		intron_variant			XP_016858277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP210L	ENST00000368559.8	c.1620+763A>G		intron_variant		5		ENSP00000357547.3
NUP210L	ENST00000271854.3	c.1620+763A>G		intron_variant		5		ENSP00000271854.3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47772 AN: 151834 Hom.: 8211 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.315 AC: 47817 AN: 151952 Hom.: 8221 Cov.: 31 AF XY: 0.321 AC XY: 23864 AN XY: 74244

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.345

Alfa AF: 0.325 Hom.: 1359

Bravo AF: 0.319

Asia WGS AF: 0.394 AC: 1368 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.49

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: rs4845597; hg19: chr1-154089438;