NM_001304533.3:c.54+98496A>G

Variant names:

• chr8-62347623-A-G
• rs4738955
• NM_001304533.3:c.54+98496A>G

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+98496A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,048 control chromosomes in the GnomAD database, including 57,855 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 0.87 (57855 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304533.3. 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
	NKAIN3	NM_001304533.3	MANE Select	c.54+98496A>G		intron	N/A	NP_001291462.1
	NKAIN3	NM_001410914.1		c.54+98496A>G		intron	N/A	NP_001397843.1
	NKAIN3	NR_130764.2		n.274+98496A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN3	ENST00000623646.3	TSL:6 MANE Select	c.54+98496A>G		intron	N/A	ENSP00000501908.1
	NKAIN3	ENST00000674864.1		c.54+98496A>G		intron	N/A	ENSP00000502526.1
	NKAIN3	ENST00000519049.6	TSL:5	c.54+98496A>G		intron	N/A	ENSP00000501734.1

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131857 AN: 151930 Hom.: 57823 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.868 AC: 131938 AN: 152048 Hom.: 57855 Cov.: 32 AF XY: 0.872 AC XY: 64788 AN XY: 74334

African (AFR) AF: 0.733 AC: 30389 AN: 41454

American (AMR) AF: 0.872 AC: 13298 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3132 AN: 3464

East Asian (EAS) AF: 0.952 AC: 4919 AN: 5168

South Asian (SAS) AF: 0.919 AC: 4439 AN: 4828

European-Finnish (FIN) AF: 0.977 AC: 10357 AN: 10596

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62485 AN: 67976

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.889 Hom.: 32694

Bravo AF: 0.854

Asia WGS AF: 0.922 AC: 3203 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.74
PhyloP100		-0.17
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: rs4738955; hg19: chr8-63260182;