8-62374707-A-G

Variant names:

• chr8-62374707-A-G
• rs16928789
• NM_001304533.3:c.54+125580A>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.54+125580A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,130 control chromosomes in the GnomAD database, including 2,627 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 (2627 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.54+125580A>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.54+125580A>G		intron_variant	Intron 1 of 6	6	NM_001304533.3	ENSP00000501908.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26257 AN: 152012 Hom.: 2619 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.173 AC: 26294 AN: 152130 Hom.: 2627 Cov.: 32 AF XY: 0.174 AC XY: 12973 AN XY: 74362

African (AFR) AF: 0.225 AC: 9336 AN: 41506

American (AMR) AF: 0.164 AC: 2509 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2085 AN: 5162

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.172 AC: 1816 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9067 AN: 67990

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.161 Hom.: 255

Bravo AF: 0.178

Asia WGS AF: 0.241 AC: 835 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.84
PhyloP100		-0.35
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: rs16928789; hg19: chr8-63287266;