rs12114607

chr8-62341854-G-Achr8-62341854-G-C

Variant summary

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

The NM_001304533.3(NKAIN3):c.54+92727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,882 control chromosomes in the GnomAD database, including 2,467 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 0.17 (2467 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.54+92727G>A		intron_variant		ENST00000623646.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.54+92727G>A		intron_variant			NM_001304533.3	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26035 AN: 151764 Hom.: 2453 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.172 AC: 26066 AN: 151882 Hom.: 2467 Cov.: 32 AF XY: 0.176 AC XY: 13027 AN XY: 74224

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.160

Alfa AF: 0.151 Hom.: 1924

Bravo AF: 0.172

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.75
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12114607; hg19: chr8-63254413;