8-63014032-T-C

Variant names:

• chr8-63014032-T-C
• rs4279586
• ENST00000524309.1:n.28-127T>C

Variant summary

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

The ENST00000524309.1(ENSG00000240915):​n.28-127T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,128 control chromosomes in the GnomAD database, including 47,593 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 0.78 (47590 hom., cov: 31)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: ENSG00000240915 ENST00000524309.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 8 publications found

Genes affected

ENSG00000240915 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986946	XR_001745930.2	n.875-127T>C		intron_variant	Intron 3 of 3
LOC107986946	XR_001745928.2	n.*24T>C		downstream_gene_variant
LOC107986946	XR_001745929.2	n.*24T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000240915	ENST00000524309.1	n.28-127T>C		intron_variant	Intron 1 of 1	5
NKAIN3	ENST00000674864.1	c.*2061T>C		downstream_gene_variant				ENSP00000502526.1
NKAIN3	ENST00000674873.1	n.*50T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118841 AN: 152002 Hom.: 47527 Cov.: 31

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 AF XY: 1.00 AC XY: 6 AN XY: 6

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.782 AC: 118963 AN: 152120 Hom.: 47590 Cov.: 31 AF XY: 0.787 AC XY: 58464 AN XY: 74330

African (AFR) AF: 0.939 AC: 39024 AN: 41538

American (AMR) AF: 0.813 AC: 12416 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2472 AN: 3466

East Asian (EAS) AF: 0.977 AC: 5048 AN: 5166

South Asian (SAS) AF: 0.874 AC: 4208 AN: 4812

European-Finnish (FIN) AF: 0.699 AC: 7372 AN: 10552

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45886 AN: 67994

Other (OTH) AF: 0.786 AC: 1660 AN: 2112

Alfa AF: 0.718 Hom.: 48724

Bravo AF: 0.797

Asia WGS AF: 0.917 AC: 3189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4279586; hg19: chr8-63926591;