rs12114607

Variant names:

• chr8-62341854-G-A
• rs12114607
• NM_001304533.3:c.54+92727G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-62341854-G-A
• chr8-62341854-G-C

Variant summary

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

The NM_001304533.3(NKAIN3):​c.54+92727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,882 control chromosomes in the GnomAD database, including 2,467 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 0.17 (2467 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.54+92727G>A		intron_variant	Intron 1 of 6	ENST00000623646.3	NP_001291462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.54+92727G>A		intron_variant	Intron 1 of 6	6	NM_001304533.3	ENSP00000501908.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26035 AN: 151764 Hom.: 2453 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.172 AC: 26066 AN: 151882 Hom.: 2467 Cov.: 32 AF XY: 0.176 AC XY: 13027 AN XY: 74224

African (AFR) AF: 0.157 AC: 6524 AN: 41446

American (AMR) AF: 0.217 AC: 3316 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2047 AN: 5114

South Asian (SAS) AF: 0.109 AC: 525 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2380 AN: 10562

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10206 AN: 67914

Other (OTH) AF: 0.160 AC: 337 AN: 2112

Alfa AF: 0.155 Hom.: 3034

Bravo AF: 0.172

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.75
DANN	Benign	0.65
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12114607; hg19: chr8-63254413;