rs1869731

Positions:

• chr8-62897128-T-C
• chr8-62897128-T-G

Variant summary

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

The NM_001304533.3(NKAIN3):​c.472-21325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,054 control chromosomes in the GnomAD database, including 45,225 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 0.77 (45225 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.472-21325T>C		intron_variant		ENST00000623646.3	NP_001291462.1
NKAIN3	NM_001410914.1	c.472-21325T>C		intron_variant			NP_001397843.1
NKAIN3	XM_017013359.2	c.472-21325T>C		intron_variant			XP_016868848.1
NKAIN3	NR_130764.2	n.692-21325T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.472-21325T>C		intron_variant			NM_001304533.3	ENSP00000501908	P1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116278 AN: 151936 Hom.: 45178 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.765 AC: 116382 AN: 152054 Hom.: 45225 Cov.: 32 AF XY: 0.771 AC XY: 57314 AN XY: 74300

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.772

Alfa AF: 0.736 Hom.: 6759

Bravo AF: 0.775

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.092
DANN	Benign	0.40

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: rs1869731; hg19: chr8-63809687;