8-63014032-T-C

Position:

• chr8-63014032-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524309.1(ENSG00000240915):​n.28-127T>C variant causes a intron, non coding transcript 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: ENST00000524309.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107986946	XR_001745930.2	n.875-127T>C		intron_variant, non_coding_transcript_variant
LOC107986946	XR_001745928.2			downstream_gene_variant
LOC107986946	XR_001745929.2			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000524309.1	n.28-127T>C		intron_variant, non_coding_transcript_variant		5
NKAIN3	ENST00000674864.1			downstream_gene_variant				ENSP00000502526
NKAIN3	ENST00000674873.1			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

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.786

Alfa AF: 0.706 Hom.: 35130

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4279586; hg19: chr8-63926591;