Variant rs4903565 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021257.4(NGB):c.89+104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,061,582 control chromosomes in the GnomAD database, including 127,841 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 0.41 ( 14744 hom., cov: 33)

Exomes 𝑓: 0.49 ( 113097 hom. )

Consequence

NGB
NM_021257.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194

Variant links:

Genes affected

NGB (HGNC:14077): (neuroglobin) This gene encodes an oxygen-binding protein that is distantly related to members of the globin gene family. It is highly conserved among other vertebrates. It is expressed in the central and peripheral nervous system where it may be involved in increasing oxygen availability and providing protection under hypoxic/ischemic conditions. [provided by RefSeq, Jul 2008]

NGB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NGB	NM_021257.4 linkuse as main transcript	c.89+104C>T		intron_variant		ENST00000298352.5	NP_067080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NGB	ENST00000298352.5 linkuse as main transcript	c.89+104C>T		intron_variant		1	NM_021257.4	ENSP00000298352	P1

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62877

AN:

152052

Hom.:

14731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.403

Gnomad FIN

AF:

0.587

Gnomad MID

AF:

0.433

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.408

GnomAD4 exome

AF:

0.492

AC:

447251

AN:

909412

Hom.:

113097

AF XY:

0.490

AC XY:

226777

AN XY:

462864

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.453

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.580

Gnomad4 NFE exome

AF:

0.521

Gnomad4 OTH exome

AF:

0.466

GnomAD4 genome

AF:

0.413

AC:

62906

AN:

152170

Hom.:

14744

Cov.:

AF XY:

0.416

AC XY:

30976

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.346

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.446

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.587

Gnomad4 NFE

AF:

0.529

Gnomad4 OTH

AF:

0.415

Alfa

AF:

0.488

Hom.:

2429

Bravo

AF:

0.384

Asia WGS

AF:

0.436

AC:

1513

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.3

DANN

Benign

0.97

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