8-62709010-A-T

Position:

• chr8-62709010-A-T

Variant summary

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

The NM_001304533.3(NKAIN3):​c.274-37922A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,172 control chromosomes in the GnomAD database, including 56,052 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 0.86 (56052 hom., cov: 33)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.274-37922A>T		intron_variant		ENST00000623646.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.274-37922A>T		intron_variant			NM_001304533.3	P1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130308 AN: 152052 Hom.: 55996 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.857 AC: 130424 AN: 152172 Hom.: 56052 Cov.: 33 AF XY: 0.855 AC XY: 63601 AN XY: 74388

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.858

Alfa AF: 0.875 Hom.: 7239

Bravo AF: 0.857

Asia WGS AF: 0.799 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44

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: rs2882926; hg19: chr8-63621569;