rs1406961

Variant names:

• chr20-63264568-A-C
• rs1406961
• ENST00000370307.6:c.-133+8014T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-63264568-A-C
• chr20-63264568-A-G
• chr20-63264568-A-T

Variant summary

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

The ENST00000370307.6(NKAIN4):​c.-133+8014T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,210 control chromosomes in the GnomAD database, including 57,402 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 0.87 (57402 hom., cov: 32)
• Consequence: NKAIN4 ENST00000370307.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 20 publications found

Genes affected

NKAIN4 (HGNC:16191): (sodium/potassium transporting ATPase interacting 4) NKAIN4 is a member of a family of mammalian proteins (see NKAIN1; MIM 612871) 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370307.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN4	ENST00000370307.6	TSL:5	c.-133+8014T>G		intron	N/A	ENSP00000359330.2	A6NNM2

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131905 AN: 152092 Hom.: 57362 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.867 AC: 132003 AN: 152210 Hom.: 57402 Cov.: 32 AF XY: 0.862 AC XY: 64154 AN XY: 74428

African (AFR) AF: 0.821 AC: 34079 AN: 41512

American (AMR) AF: 0.831 AC: 12716 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3148 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4714 AN: 5178

South Asian (SAS) AF: 0.870 AC: 4199 AN: 4828

European-Finnish (FIN) AF: 0.825 AC: 8737 AN: 10588

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61535 AN: 68014

Other (OTH) AF: 0.865 AC: 1829 AN: 2114

Alfa AF: 0.893 Hom.: 217182

Bravo AF: 0.868

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1406961; hg19: chr20-61895920;