8-62483421-A-T

Variant names:

• chr8-62483421-A-T
• rs1993126
• NM_001304533.3:c.55-96118A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001304533.3(NKAIN3):​c.55-96118A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NKAIN3 NM_001304533.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50
• Publications: 0 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]

ENSG00000253975 (HGNC:58637):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304533.3. 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
	NKAIN3	NM_001304533.3	MANE Select	c.55-96118A>T		intron	N/A	NP_001291462.1	A0A6Q8PFP9
	NKAIN3	NM_001410914.1		c.55-96118A>T		intron	N/A	NP_001397843.1	A0A6Q8PGC9
	NKAIN3	NR_130764.2		n.275-96118A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN3	ENST00000623646.3	TSL:6 MANE Select	c.55-96118A>T		intron	N/A	ENSP00000501908.1	A0A6Q8PFP9
	NKAIN3	ENST00000674864.1		c.55-96118A>T		intron	N/A	ENSP00000502526.1	A0A6Q8PH17
	NKAIN3	ENST00000519049.6	TSL:5	c.55-96118A>T		intron	N/A	ENSP00000501734.1	A0A6Q8PFE2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 50270 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 28510

African (AFR) AF: 0.00 AC: 0 AN: 1664

American (AMR) AF: 0.00 AC: 0 AN: 5518

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 762

East Asian (EAS) AF: 0.00 AC: 0 AN: 3334

South Asian (SAS) AF: 0.00 AC: 0 AN: 4626

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5174

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 86

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26862

Other (OTH) AF: 0.00 AC: 0 AN: 2244

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.48
PhyloP100		2.5

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: rs1993126; hg19: chr8-63395980;