rs1869733

Variant names:

• chr8-62895841-C-T
• rs1869733
• NM_001304533.3:c.472-22612C>T

Variant summary

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

The NM_001304533.3(NKAIN3):​c.472-22612C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,004 control chromosomes in the GnomAD database, including 3,927 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 0.21 (3927 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.472-22612C>T		intron_variant	Intron 4 of 6	ENST00000623646.3	NP_001291462.1
NKAIN3	NM_001410914.1	c.472-22612C>T		intron_variant	Intron 4 of 5		NP_001397843.1
NKAIN3	NR_130764.2	n.692-22612C>T		intron_variant	Intron 4 of 6
NKAIN3	XM_017013359.2	c.472-22612C>T		intron_variant	Intron 4 of 5		XP_016868848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.472-22612C>T		intron_variant	Intron 4 of 6	6	NM_001304533.3	ENSP00000501908.1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31720 AN: 151886 Hom.: 3919 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.209 AC: 31734 AN: 152004 Hom.: 3927 Cov.: 32 AF XY: 0.216 AC XY: 16035 AN XY: 74284

African (AFR) AF: 0.162 AC: 6710 AN: 41490

American (AMR) AF: 0.348 AC: 5304 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2793 AN: 5138

South Asian (SAS) AF: 0.193 AC: 927 AN: 4814

European-Finnish (FIN) AF: 0.237 AC: 2502 AN: 10568

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12074 AN: 67960

Other (OTH) AF: 0.222 AC: 469 AN: 2116

Alfa AF: 0.195 Hom.: 4465

Bravo AF: 0.222

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.46
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: rs1869733; hg19: chr8-63808400;