8-62909881-A-G

Variant names:

• chr8-62909881-A-G
• rs1455576
• NM_001304533.3:c.472-8572A>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.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
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.472-8572A>G		intron_variant	Intron 4 of 6	ENST00000623646.3	NP_001291462.1
NKAIN3	NM_001410914.1	c.472-8572A>G		intron_variant	Intron 4 of 5		NP_001397843.1
NKAIN3	NR_130764.2	n.692-8572A>G		intron_variant	Intron 4 of 6
NKAIN3	XM_017013359.2	c.472-8572A>G		intron_variant	Intron 4 of 5		XP_016868848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.472-8572A>G		intron_variant	Intron 4 of 6	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

African (AFR) AF: 0.558 AC: 23136 AN: 41448

American (AMR) AF: 0.577 AC: 8790 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3690 AN: 5174

South Asian (SAS) AF: 0.529 AC: 2551 AN: 4818

European-Finnish (FIN) AF: 0.614 AC: 6476 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32771 AN: 67870

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.491 Hom.: 61113

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
PhyloP100		0.33
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: rs1455576; hg19: chr8-63822440;