Variant rs888208 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_145285.3(NKX2-3):c.*385A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 228,802 control chromosomes in the GnomAD database, including 8,356 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 0.25 ( 5497 hom., cov: 33)

Exomes 𝑓: 0.25 ( 2859 hom. )

Consequence

NKX2-3
NM_145285.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.631

Variant links:

Genes affected

NKX2-3 (HGNC:7836): (NK2 homeobox 3) This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]

NKX2-3 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKX2-3	NM_145285.3 linkuse as main transcript	c.*385A>G		3_prime_UTR_variant	2/2	ENST00000344586.9	NP_660328.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKX2-3	ENST00000344586.9 linkuse as main transcript	c.*385A>G		3_prime_UTR_variant	2/2	2	NM_145285.3	ENSP00000342828	P1

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38279

AN:

152146

Hom.:

5494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.252

GnomAD4 exome

AF:

0.246

AC:

18808

AN:

76538

Hom.:

2859

Cov.:

AF XY:

0.238

AC XY:

9415

AN XY:

39550

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.411

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.340

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.235

GnomAD4 genome

AF:

0.251

AC:

38288

AN:

152264

Hom.:

5497

Cov.:

AF XY:

0.257

AC XY:

19165

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.270

Hom.:

4222

Bravo

AF:

0.240

Asia WGS

AF:

0.292

AC:

1017

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.5

DANN

Benign

0.54

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