NM_207308.3:c.4931-160G>A

Variant names:

• chr1-154002145-C-T
• rs6701341
• NM_207308.3:c.4931-160G>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.4931-160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,028 control chromosomes in the GnomAD database, including 6,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.28 (6307 hom., cov: 32)
• Consequence: NUP210L NM_207308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 12 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP210L	NM_207308.3	MANE Select	c.4931-160G>A		intron	N/A	NP_997191.2
	NUP210L	NM_001159484.1		c.4931-6965G>A		intron	N/A	NP_001152956.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUP210L	ENST00000368559.8	TSL:5 MANE Select	c.4931-160G>A		intron	N/A	ENSP00000357547.3
	NUP210L	ENST00000368553.5	TSL:1	c.1730-6965G>A		intron	N/A	ENSP00000357541.1
	NUP210L	ENST00000271854.3	TSL:5	c.4931-6965G>A		intron	N/A	ENSP00000271854.3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42227 AN: 151910 Hom.: 6299 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.278 AC: 42264 AN: 152028 Hom.: 6307 Cov.: 32 AF XY: 0.283 AC XY: 21059 AN XY: 74294

African (AFR) AF: 0.164 AC: 6798 AN: 41492

American (AMR) AF: 0.393 AC: 5990 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1457 AN: 5174

South Asian (SAS) AF: 0.344 AC: 1661 AN: 4822

European-Finnish (FIN) AF: 0.342 AC: 3602 AN: 10534

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20770 AN: 67968

Other (OTH) AF: 0.303 AC: 638 AN: 2108

Alfa AF: 0.300 Hom.: 2009

Bravo AF: 0.278

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.17
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: rs6701341; hg19: chr1-153974621; COSMIC: COSV55144183;