rs6701341

Positions:

• chr1-154002145-C-T

Variant summary

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

The ENST00000368559.8(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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6307 hom., cov: 32)
• Consequence: NUP210L ENST00000368559.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUP210L	NM_207308.3	c.4931-160G>A		intron_variant		ENST00000368559.8	NP_997191.2
NUP210L	XM_011510122.2	c.4799-160G>A		intron_variant			XP_011508424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP210L	ENST00000368559.8	c.4931-160G>A		intron_variant		5	NM_207308.3	ENSP00000357547	P2
NUP210L	ENST00000368553.5	c.1730-6965G>A		intron_variant		1		ENSP00000357541	A2
NUP210L	ENST00000271854.3	c.4931-6965G>A		intron_variant		5		ENSP00000271854	A2

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

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.303

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.38

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: rs6701341; hg19: chr1-153974621; COSMIC: COSV55144183;