rs142014203

chr8-62346358-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001304533.3(NKAIN3):c.54+97231T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 152,126 control chromosomes in the GnomAD database, including 64 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 0.021 (64 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0213 (3245/152126) while in subpopulation NFE AF= 0.0335 (2279/67966). AF 95% confidence interval is 0.0324. There are 64 homozygotes in gnomad4. There are 1485 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 63 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.54+97231T>G		intron_variant		ENST00000623646.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.54+97231T>G		intron_variant			NM_001304533.3	P1

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3245 AN: 152008 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.00565

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0213 AC: 3245 AN: 152126 Hom.: 64 Cov.: 32 AF XY: 0.0200 AC XY: 1485 AN XY: 74368

Gnomad4 AFR AF: 0.00566

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00643

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0354

Alfa AF: 0.0251 Hom.: 7

Bravo AF: 0.0236

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs142014203; hg19: chr8-63258917;