rs10496684

Positions:

• chr2-131603900-C-T

Variant summary

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

The NR_033885.3(POTEKP):​n.594-118C>T 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 0.409 in 928,214 control chromosomes in the GnomAD database, including 80,253 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 0.40 (12549 hom., cov: 34)
  • Exomes 𝑓: 0.41 (67704 hom.)
• Consequence: POTEKP NR_033885.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

Genes affected

POTEKP (HGNC:30182): (POTE ankyrin domain family member K, pseudogene) Predicted to be a structural constituent of postsynaptic actin cytoskeleton. Predicted to be involved in postsynaptic actin cytoskeleton organization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POTEKP	NR_033885.3	n.594-118C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POTEKP	ENST00000397487.4	n.884-118C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61325 AN: 151946 Hom.: 12541 Cov.: 34

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.419

GnomAD4 exome AF: 0.410 AC: 318527 AN: 776150 Hom.: 67704 AF XY: 0.412 AC XY: 162500 AN XY: 394090

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.325

Gnomad4 ASJ exome AF: 0.429

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.457

Gnomad4 FIN exome AF: 0.386

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.417

GnomAD4 genome AF: 0.404 AC: 61370 AN: 152064 Hom.: 12549 Cov.: 34 AF XY: 0.404 AC XY: 30010 AN XY: 74318

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.416

Alfa AF: 0.406 Hom.: 1573

Bravo AF: 0.403

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496684; hg19: chr2-132361473; COSMIC: COSV68746183;