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. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN4	ENST00000370307.6	c.-133+8014T>G		intron_variant	Intron 1 of 6	5		ENSP00000359330.2

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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.865

Alfa AF: 0.898 Hom.: 138024

Bravo AF: 0.868

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406961; hg19: chr20-61895920;