rs2351667

Positions:

• chr8-62365650-G-A

Variant summary

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

The NM_001304533.3(NKAIN3):​c.54+116523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,192 control chromosomes in the GnomAD database, including 52,799 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 0.83 (52799 hom., cov: 33)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.54+116523G>A		intron_variant		ENST00000623646.3	NP_001291462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.54+116523G>A		intron_variant			NM_001304533.3	ENSP00000501908	P1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126407 AN: 152074 Hom.: 52766 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.831 AC: 126491 AN: 152192 Hom.: 52799 Cov.: 33 AF XY: 0.829 AC XY: 61671 AN XY: 74384

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.833

Alfa AF: 0.850 Hom.: 108122

Bravo AF: 0.829

Asia WGS AF: 0.749 AC: 2604 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.65

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: rs2351667; hg19: chr8-63278209;