Variant rs1406961 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000370307.6(NKAIN4):c.-133+8014T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,210 control chromosomes in the GnomAD database, including 57,402 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 0.87 ( 57402 hom., cov: 32)

Consequence

NKAIN4
ENST00000370307.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

Variant links:

Genes affected

NKAIN4 (HGNC:16191): (sodium/potassium transporting ATPase interacting 4) NKAIN4 is a member of a family of mammalian proteins (see NKAIN1; MIM 612871) with similarity to Drosophila Nkain and interacts with the beta subunit of Na,K-ATPase (ATP1B1; MIM 182330) (Gorokhova et al., 2007 [PubMed 17606467]).[supplied by OMIM, Jun 2009]

NKAIN4 links:

(HGNC:):

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.63264568A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN4	ENST00000370307.6 linkuse as main transcript	c.-133+8014T>G		intron_variant		5		ENSP00000359330.2		A6NNM2

Frequencies

GnomAD3 genomes

AF:

0.867

AC:

131905

AN:

152092

Hom.:

57362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.867

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.907

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.870

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.883

Gnomad NFE

AF:

0.905

Gnomad OTH

AF:

0.864

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.867

AC:

132003

AN:

152210

Hom.:

57402

Cov.:

AF XY:

0.862

AC XY:

64154

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.821

Gnomad4 AMR

AF:

0.831

Gnomad4 ASJ

AF:

0.907

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.870

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.905

Gnomad4 OTH

AF:

0.865

Alfa

AF:

0.898

Hom.:

138024

Bravo

AF:

0.868

Asia WGS

AF:

0.885

AC:

3078

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.2

DANN

Benign

0.50

Splicing

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