rs9332437

chr8-62840182-C-T

Variant summary

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

The NM_001304533.3(NKAIN3):c.472-78271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,780 control chromosomes in the GnomAD database, including 28,450 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 0.60 (28450 hom., cov: 30)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.472-78271C>T		intron_variant		ENST00000623646.3
NKAIN3	NM_001410914.1	c.472-78271C>T		intron_variant
NKAIN3	XM_017013359.2	c.472-78271C>T		intron_variant
NKAIN3	NR_130764.2	n.692-78271C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.472-78271C>T		intron_variant			NM_001304533.3	P1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91530 AN: 151662 Hom.: 28429 Cov.: 30

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.603 AC: 91586 AN: 151780 Hom.: 28450 Cov.: 30 AF XY: 0.596 AC XY: 44172 AN XY: 74174

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.615

Alfa AF: 0.643 Hom.: 3963

Bravo AF: 0.591

Asia WGS AF: 0.477 AC: 1654 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.4
Dann	Benign	0.69

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: rs9332437; hg19: chr8-63752741;