8-62971034-C-T

Variant names:

• chr8-62971034-C-T
• rs7834588
• NM_001304533.3:c.*5627C>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.*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
• Publications: 14 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=-0.88).
• 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 rank	MANE	Protein	UniProt
NKAIN3	NM_001304533.3	c.*5627C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000623646.3	NP_001291462.1
NKAIN3	NR_130764.2	n.753-19134C>T		intron_variant	Intron 5 of 6
NKAIN3	XM_017013359.2	c.533-28197C>T		intron_variant	Intron 5 of 5		XP_016868848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN3	ENST00000623646.3	c.*5627C>T		3_prime_UTR_variant	Exon 7 of 7	6	NM_001304533.3	ENSP00000501908.1

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

African (AFR) AF: 0.459 AC: 18844 AN: 41064

American (AMR) AF: 0.366 AC: 5549 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2182 AN: 5056

South Asian (SAS) AF: 0.476 AC: 2267 AN: 4762

European-Finnish (FIN) AF: 0.374 AC: 3921 AN: 10478

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23134 AN: 67910

Other (OTH) AF: 0.355 AC: 747 AN: 2106

Alfa AF: 0.348 Hom.: 38876

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
PhyloP100		-0.14
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: rs7834588; hg19: chr8-63883593;