Variant 1-154000695-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_207308.3(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
NM_207308.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	Effect	Protein	UniProt
NUP210L	NM_207308.3 link	c.5386+161G>A	intron_variant	NP_997191.2	Q5VU65-1
NUP210L	NM_001159484.1 link	c.4931-5515G>A	intron_variant	NP_001152956.1	Q5VU65-2
NUP210L	XM_017002788.3 link	c.5386+161G>A	intron_variant	XP_016858277.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
NUP210L	ENST00000368559.8 link	c.5386+161G>A	intron_variant	5	ENSP00000357547.3	Q5VU65-1
NUP210L	ENST00000368553.5 link	c.1730-5515G>A	intron_variant	1	ENSP00000357541.1	X6R6V8
NUP210L	ENST00000271854.3 link	c.4931-5515G>A	intron_variant	5	ENSP00000271854.3	Q5VU65-2

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22471

AN:

152068

Hom.:

2045

Cov.:

show subpopulations

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.:

AF XY:

0.151

AC XY:

11220

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.0822

Gnomad4 EAS

AF:

0.493

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.137

Alfa

AF:

0.121

Hom.:

1242

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over