8-62971034-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304533.3(NKAIN3):c.*5627C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,214 control chromosomes in the GnomAD database, including 11,331 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 0.38 (11331 hom., cov: 32)
• Consequence: NKAIN3 NM_001304533.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN3	NM_001304533.3	c.*5627C>T		3_prime_UTR_variant	7/7	ENST00000623646.3
NKAIN3	XM_017013359.2	c.533-28197C>T		intron_variant
NKAIN3	NR_130764.2	n.753-19134C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000623646.3	c.*5627C>T		3_prime_UTR_variant	7/7		NM_001304533.3	P1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57935 AN: 151096 Hom.: 11301 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.384 AC: 58010 AN: 151214 Hom.: 11331 Cov.: 32 AF XY: 0.385 AC XY: 28429 AN XY: 73838

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.355

Alfa AF: 0.341 Hom.: 18209

Bravo AF: 0.380

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.8
Dann	Benign	0.60

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: rs7834588; hg19: chr8-63883593;