chr8-62483421-A-G

Variant names:

• chr8-62483421-A-G
• rs1993126
• NM_001304533.3:c.55-96118A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ENSG00000253975 (HGNC:58637):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.55-96118A>G		intron_variant	Intron 1 of 6	ENST00000623646.3	NP_001291462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.55-96118A>G		intron_variant	Intron 1 of 6	6	NM_001304533.3	ENSP00000501908.1

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

African (AFR) AF: 0.883 AC: 1469 AN: 1664

American (AMR) AF: 0.826 AC: 4539 AN: 5496

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 696 AN: 760

East Asian (EAS) AF: 0.815 AC: 2707 AN: 3320

South Asian (SAS) AF: 0.905 AC: 4175 AN: 4614

European-Finnish (FIN) AF: 0.867 AC: 4473 AN: 5162

Middle Eastern (MID) AF: 0.884 AC: 76 AN: 86

European-Non Finnish (NFE) AF: 0.861 AC: 23078 AN: 26804

Other (OTH) AF: 0.874 AC: 1961 AN: 2244

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

African (AFR) AF: 0.878 AC: 36385 AN: 41450

American (AMR) AF: 0.856 AC: 13083 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3108 AN: 3470

East Asian (EAS) AF: 0.789 AC: 4046 AN: 5128

South Asian (SAS) AF: 0.890 AC: 4282 AN: 4810

European-Finnish (FIN) AF: 0.853 AC: 8999 AN: 10552

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58927 AN: 67976

Other (OTH) AF: 0.870 AC: 1836 AN: 2110

Alfa AF: 0.865 Hom.: 7361

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
PhyloP100		2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1993126; hg19: chr8-63395980;