8-63010855-A-G

Variant names:

• chr8-63010855-A-G
• rs12548933
• ENST00000674864.1:c.*16-1132A>G

Variant summary

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

The ENST00000674864.1(NKAIN3):​c.*16-1132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,208 control chromosomes in the GnomAD database, including 2,660 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 0.18 (2660 hom., cov: 32)
• Consequence: NKAIN3 ENST00000674864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 2 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]

LOC107986946 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674864.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN3	ENST00000674864.1		c.*16-1132A>G		intron	N/A	ENSP00000502526.1
	NKAIN3	ENST00000674873.1		n.493-1132A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27355 AN: 152090 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.180 AC: 27395 AN: 152208 Hom.: 2660 Cov.: 32 AF XY: 0.183 AC XY: 13639 AN XY: 74426

African (AFR) AF: 0.161 AC: 6675 AN: 41510

American (AMR) AF: 0.214 AC: 3275 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2190 AN: 5176

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4818

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10608

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11129 AN: 68014

Other (OTH) AF: 0.171 AC: 361 AN: 2114

Alfa AF: 0.166 Hom.: 2713

Bravo AF: 0.186

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.41
PhyloP100		-0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12548933; hg19: chr8-63923414;