NM_024522.3:c.54+13339T>C

Variant names:

• chr1-31226155-A-G
• rs10914332
• NM_024522.3:c.54+13339T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024522.3(NKAIN1):​c.54+13339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,280 control chromosomes in the GnomAD database, including 3,738 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 0.21 (3738 hom., cov: 33)
• Consequence: NKAIN1 NM_024522.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 5 publications found

Genes affected

NKAIN1 (HGNC:25743): (sodium/potassium transporting ATPase interacting 1) NKAIN1 is a member of a family of mammalian proteins with similarity to Drosophila Nkain and interacts with the beta subunit of Na,K-ATPase (ATP1B1; MIM 182330) (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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN1	NM_024522.3	c.54+13339T>C		intron_variant	Intron 1 of 6	ENST00000373736.7	NP_078798.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN1	ENST00000373736.7	c.54+13339T>C		intron_variant	Intron 1 of 6	2	NM_024522.3	ENSP00000362841.2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31527 AN: 152162 Hom.: 3728 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.207 AC: 31566 AN: 152280 Hom.: 3738 Cov.: 33 AF XY: 0.209 AC XY: 15530 AN XY: 74470

African (AFR) AF: 0.320 AC: 13274 AN: 41532

American (AMR) AF: 0.140 AC: 2144 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1082 AN: 5192

South Asian (SAS) AF: 0.232 AC: 1122 AN: 4830

European-Finnish (FIN) AF: 0.176 AC: 1865 AN: 10610

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

European-Non Finnish (NFE) AF: 0.164 AC: 11121 AN: 68018

Other (OTH) AF: 0.192 AC: 406 AN: 2114

Alfa AF: 0.174 Hom.: 8026

Bravo AF: 0.208

Asia WGS AF: 0.269 AC: 933 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	9.6
DANN	Benign	0.54
PhyloP100		0.72
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: rs10914332; hg19: chr1-31699002;