1-154000695-C-T

Variant names:

• chr1-154000695-C-T
• rs11264824
• ENST00000368559.8:c.5386+161G>A

Variant summary

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

The ENST00000368559.8(NUP210L):​c.5386+161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,186 control chromosomes in the GnomAD database, including 2,041 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 0.15 (2041 hom., cov: 32)
• Consequence: NUP210L ENST00000368559.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP210L	NM_207308.3	c.5386+161G>A		intron_variant	Intron 37 of 39		NP_997191.2
NUP210L	NM_001159484.1	c.4931-5515G>A		intron_variant	Intron 35 of 37		NP_001152956.1
NUP210L	XM_017002788.3	c.5386+161G>A		intron_variant	Intron 37 of 38		XP_016858277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP210L	ENST00000368559.8	c.5386+161G>A		intron_variant	Intron 37 of 39	5		ENSP00000357547.3
NUP210L	ENST00000368553.5	c.1730-5515G>A		intron_variant	Intron 13 of 15	1		ENSP00000357541.1
NUP210L	ENST00000271854.3	c.4931-5515G>A		intron_variant	Intron 35 of 37	5		ENSP00000271854.3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22471 AN: 152068 Hom.: 2045 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.148 AC: 22464 AN: 152186 Hom.: 2041 Cov.: 32 AF XY: 0.151 AC XY: 11220 AN XY: 74382

African (AFR) AF: 0.149 AC: 6202 AN: 41524

American (AMR) AF: 0.102 AC: 1565 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2548 AN: 5164

South Asian (SAS) AF: 0.152 AC: 733 AN: 4828

European-Finnish (FIN) AF: 0.193 AC: 2043 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8554 AN: 68016

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.127 Hom.: 2116

Bravo AF: 0.143

Asia WGS AF: 0.293 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.30
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: rs11264824; hg19: chr1-153973171; COSMIC: COSV55147020; COSMIC: COSV55147020;