Variant chr14-24407955-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_025081.3(NYNRIN):c.285A>G(p.Gln95=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0522 in 1,613,960 control chromosomes in the GnomAD database, including 2,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.041 ( 168 hom., cov: 33)

Exomes 𝑓: 0.053 ( 2421 hom. )

Consequence

NYNRIN
NM_025081.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.250

Variant links:

Genes affected

NYNRIN (HGNC:20165): (NYN domain and retroviral integrase containing) Predicted to enable endoribonuclease activity and mRNA binding activity. Predicted to be involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Predicted to be integral component of membrane. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NYNRIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 14-24407955-A-G is Benign according to our data. Variant chr14-24407955-A-G is described in ClinVar as [Benign]. Clinvar id is 2846466.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NYNRIN	NM_025081.3 linkuse as main transcript	c.285A>G	p.Gln95=	synonymous_variant	3/9	ENST00000382554.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NYNRIN	ENST00000382554.4 linkuse as main transcript	c.285A>G	p.Gln95=	synonymous_variant	3/9	5	NM_025081.3	P1	Q9P2P1-1

Frequencies

GnomAD3 genomes

AF:

0.0410

AC:

6235

AN:

152212

Hom.:

169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0374

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0600

Gnomad FIN

AF:

0.0502

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0557

Gnomad OTH

AF:

0.0497

GnomAD3 exomes

AF:

0.0489

AC:

12179

AN:

249158

Hom.:

409

AF XY:

0.0516

AC XY:

6978

AN XY:

135154

show subpopulations

Gnomad AFR exome

AF:

0.00917

Gnomad AMR exome

AF:

0.0281

Gnomad ASJ exome

AF:

0.124

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0675

Gnomad FIN exome

AF:

0.0512

Gnomad NFE exome

AF:

0.0556

Gnomad OTH exome

AF:

0.0611

GnomAD4 exome

AF:

0.0534

AC:

78037

AN:

1461630

Hom.:

2421

Cov.:

AF XY:

0.0543

AC XY:

39467

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.00893

Gnomad4 AMR exome

AF:

0.0291

Gnomad4 ASJ exome

AF:

0.126

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0681

Gnomad4 FIN exome

AF:

0.0547

Gnomad4 NFE exome

AF:

0.0547

Gnomad4 OTH exome

AF:

0.0540

GnomAD4 genome

AF:

0.0409

AC:

6235

AN:

152330

Hom.:

168

Cov.:

AF XY:

0.0411

AC XY:

3061

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0112

Gnomad4 AMR

AF:

0.0374

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0603

Gnomad4 FIN

AF:

0.0502

Gnomad4 NFE

AF:

0.0557

Gnomad4 OTH

AF:

0.0487

Alfa

AF:

0.0544

Hom.:

132

Bravo

AF:

0.0377

Asia WGS

AF:

0.0250

AC:

AN:

3478

EpiCase

AF:

0.0575

EpiControl

AF:

0.0595

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

8.5

DANN

Benign

0.41

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over