rs1993126

chr8-62483421-A-Gchr8-62483421-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304533.3(NKAIN3):c.55-96118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 202,130 control chromosomes in the GnomAD database, including 75,733 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 (57124 hom., cov: 30)
  • Exomes 𝑓: 0.86 (18609 hom.)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

Genes affected

NKAIN3 (HGNC:26829): (sodium/potassium transporting ATPase interacting 3) NKAIN3 is a member of a family of mammalian proteins (see NKAIN1; MIM 612871) with similarity to Drosophila Nkain (Gorokhova et al., 2007 [PubMed 17606467]).[supplied by OMIM, Jun 2009]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.55-96118A>G		intron_variant		ENST00000623646.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.55-96118A>G		intron_variant			NM_001304533.3	P1
	ENST00000518404.1	n.391T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131575 AN: 151860 Hom.: 57081 Cov.: 30

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.869

GnomAD4 exome AF: 0.861 AC: 43174 AN: 50150 Hom.: 18609 Cov.: 0 AF XY: 0.866 AC XY: 24643 AN XY: 28446

Gnomad4 AFR exome AF: 0.883

Gnomad4 AMR exome AF: 0.826

Gnomad4 ASJ exome AF: 0.916

Gnomad4 EAS exome AF: 0.815

Gnomad4 SAS exome AF: 0.905

Gnomad4 FIN exome AF: 0.867

Gnomad4 NFE exome AF: 0.861

Gnomad4 OTH exome AF: 0.874

GnomAD4 genome AF: 0.866 AC: 131671 AN: 151980 Hom.: 57124 Cov.: 30 AF XY: 0.865 AC XY: 64280 AN XY: 74282

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.870

Alfa AF: 0.865 Hom.: 7068

Bravo AF: 0.866

Asia WGS AF: 0.843 AC: 2934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	8.2
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs1993126; hg19: chr8-63395980;