8-62361384-C-T

Variant names:

• chr8-62361384-C-T
• rs16928749
• NM_001304533.3:c.54+112257C>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.54+112257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,234 control chromosomes in the GnomAD database, including 1,357 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 0.12 (1357 hom., cov: 35)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN3	NM_001304533.3	MANE Select	c.54+112257C>T		intron	N/A	NP_001291462.1	A0A6Q8PFP9
	NKAIN3	NM_001410914.1		c.54+112257C>T		intron	N/A	NP_001397843.1	A0A6Q8PGC9
	NKAIN3	NR_130764.2		n.274+112257C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN3	ENST00000623646.3	TSL:6 MANE Select	c.54+112257C>T		intron	N/A	ENSP00000501908.1	A0A6Q8PFP9
	NKAIN3	ENST00000674864.1		c.54+112257C>T		intron	N/A	ENSP00000502526.1	A0A6Q8PH17
	NKAIN3	ENST00000519049.6	TSL:5	c.54+112257C>T		intron	N/A	ENSP00000501734.1	A0A6Q8PFE2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18363 AN: 152116 Hom.: 1349 Cov.: 35

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18387 AN: 152234 Hom.: 1357 Cov.: 35 AF XY: 0.124 AC XY: 9207 AN XY: 74428

African (AFR) AF: 0.0958 AC: 3980 AN: 41542

American (AMR) AF: 0.131 AC: 2007 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2012 AN: 5172

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10600

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

European-Non Finnish (NFE) AF: 0.110 AC: 7487 AN: 68016

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.110 Hom.: 1483

Bravo AF: 0.121

Asia WGS AF: 0.227 AC: 788 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.097
DANN	Benign	0.62
PhyloP100		-3.0
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: rs16928749; hg19: chr8-63273943;