rs12548933

Positions:

• chr8-63010855-A-G

Variant summary

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

The XR_001745930.2(LOC107986946):​n.555-1132A>G 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 0.18 in 152,208 control chromosomes in the GnomAD database, including 2,660 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 0.18 (2660 hom., cov: 32)
• Consequence: LOC107986946 XR_001745930.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

Genes affected

LOC107986946 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986946	XR_001745930.2	n.555-1132A>G		intron_variant, non_coding_transcript_variant
LOC107986946	XR_001745928.2	n.555-1132A>G		intron_variant, non_coding_transcript_variant
LOC107986946	XR_001745929.2	n.555-1132A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN3	ENST00000674864.1	c.*16-1132A>G		intron_variant
NKAIN3	ENST00000674873.1	n.493-1132A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27355 AN: 152090 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.180 AC: 27395 AN: 152208 Hom.: 2660 Cov.: 32 AF XY: 0.183 AC XY: 13639 AN XY: 74426

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.171

Alfa AF: 0.164 Hom.: 2068

Bravo AF: 0.186

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12548933; hg19: chr8-63923414;