8-62909881-A-G

Position:

• chr8-62909881-A-G

Variant summary

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

The NM_001304533.3(NKAIN3):​c.472-8572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,882 control chromosomes in the GnomAD database, including 21,779 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 0.53 (21779 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

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]

NKAIN3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.472-8572A>G		intron_variant		ENST00000623646.3	NP_001291462.1
NKAIN3	NM_001410914.1	c.472-8572A>G		intron_variant			NP_001397843.1
NKAIN3	XM_017013359.2	c.472-8572A>G		intron_variant			XP_016868848.1
NKAIN3	NR_130764.2	n.692-8572A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.472-8572A>G		intron_variant		6	NM_001304533.3	ENSP00000501908.1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80564 AN: 151764 Hom.: 21739 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.531 AC: 80645 AN: 151882 Hom.: 21779 Cov.: 32 AF XY: 0.538 AC XY: 39959 AN XY: 74212

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.526

Alfa AF: 0.482 Hom.: 36039

Bravo AF: 0.532

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.64

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: rs1455576; hg19: chr8-63822440;