8-62928537-T-C

Variant names:

• chr8-62928537-T-C
• rs4134468
• NM_001304533.3:c.532+10024T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304533.3(NKAIN3):​c.532+10024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,044 control chromosomes in the GnomAD database, including 22,640 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 0.54 (22640 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.532+10024T>C		intron_variant	Intron 5 of 6	ENST00000623646.3	NP_001291462.1
NKAIN3	NM_001410914.1	c.532+10024T>C		intron_variant	Intron 5 of 5		NP_001397843.1
NKAIN3	NR_130764.2	n.752+10024T>C		intron_variant	Intron 5 of 6
NKAIN3	XM_017013359.2	c.532+10024T>C		intron_variant	Intron 5 of 5		XP_016868848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.532+10024T>C		intron_variant	Intron 5 of 6	6	NM_001304533.3	ENSP00000501908.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82302 AN: 151926 Hom.: 22593 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.542 AC: 82391 AN: 152044 Hom.: 22640 Cov.: 32 AF XY: 0.549 AC XY: 40804 AN XY: 74312

African (AFR) AF: 0.576 AC: 23871 AN: 41478

American (AMR) AF: 0.590 AC: 9024 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3662 AN: 5146

South Asian (SAS) AF: 0.544 AC: 2623 AN: 4824

European-Finnish (FIN) AF: 0.616 AC: 6504 AN: 10566

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33338 AN: 67962

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.502 Hom.: 10096

Bravo AF: 0.543

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.59
PhyloP100		0.89
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: rs4134468; hg19: chr8-63841096;