8-62381022-G-A

Variant names:

• chr8-62381022-G-A
• rs6472025
• NM_001304533.3:c.54+131895G>A

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+131895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,280 control chromosomes in the GnomAD database, including 71,618 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 0.97 (71618 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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+131895G>A		intron	N/A	NP_001291462.1
	NKAIN3	NM_001410914.1		c.54+131895G>A		intron	N/A	NP_001397843.1
	NKAIN3	NR_130764.2		n.274+131895G>A		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+131895G>A		intron	N/A	ENSP00000501908.1
	NKAIN3	ENST00000674864.1		c.54+131895G>A		intron	N/A	ENSP00000502526.1
	NKAIN3	ENST00000519049.6	TSL:5	c.54+131895G>A		intron	N/A	ENSP00000501734.1

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147518 AN: 152162 Hom.: 71564 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.982

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.969 AC: 147631 AN: 152280 Hom.: 71618 Cov.: 32 AF XY: 0.970 AC XY: 72232 AN XY: 74474

African (AFR) AF: 0.929 AC: 38582 AN: 41538

American (AMR) AF: 0.982 AC: 15021 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3427 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5182

South Asian (SAS) AF: 0.977 AC: 4715 AN: 4828

European-Finnish (FIN) AF: 0.987 AC: 10486 AN: 10620

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66976 AN: 68026

Other (OTH) AF: 0.972 AC: 2055 AN: 2114

Alfa AF: 0.976 Hom.: 9368

Bravo AF: 0.968

Asia WGS AF: 0.984 AC: 3418 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.38
PhyloP100		1.1
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: rs6472025; hg19: chr8-63293581;