8-62928537-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.532+10024T>C		intron_variant		ENST00000623646.3
NKAIN3	NM_001410914.1	c.532+10024T>C		intron_variant
NKAIN3	XM_017013359.2	c.532+10024T>C		intron_variant
NKAIN3	NR_130764.2	n.752+10024T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.532+10024T>C		intron_variant			NM_001304533.3	P1

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.539

Alfa AF: 0.502 Hom.: 9029

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

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: rs4134468; hg19: chr8-63841096;