2-131603900-C-T

Variant names:

• chr2-131603900-C-T
• rs10496684
• ENST00000397487.4:n.884-118C>T

Variant summary

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

The ENST00000397487.4(POTEKP):​n.884-118C>T variant causes a intron 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 ENST00000397487.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 2 publications found

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]

ENSG00000286208 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
POTEKP	NR_033885.3	n.594-118C>T		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POTEKP	ENST00000397487.4	n.884-118C>T		intron_variant	Intron 5 of 10	6
ENSG00000286208	ENST00000727992.1	n.1713-118C>T		intron_variant	Intron 11 of 13
ENSG00000286208	ENST00000727993.1	n.1102-118C>T		intron_variant	Intron 5 of 6

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

African (AFR) AF: 0.396 AC: 6927 AN: 17490

American (AMR) AF: 0.325 AC: 6541 AN: 20108

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 6436 AN: 15008

East Asian (EAS) AF: 0.356 AC: 8208 AN: 23034

South Asian (SAS) AF: 0.457 AC: 26069 AN: 57028

European-Finnish (FIN) AF: 0.386 AC: 12331 AN: 31948

Middle Eastern (MID) AF: 0.476 AC: 1058 AN: 2224

European-Non Finnish (NFE) AF: 0.412 AC: 237286 AN: 576496

Other (OTH) AF: 0.417 AC: 13671 AN: 32814

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

African (AFR) AF: 0.396 AC: 16424 AN: 41472

American (AMR) AF: 0.369 AC: 5634 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3472

East Asian (EAS) AF: 0.352 AC: 1821 AN: 5180

South Asian (SAS) AF: 0.453 AC: 2182 AN: 4820

European-Finnish (FIN) AF: 0.389 AC: 4115 AN: 10568

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28244 AN: 67970

Other (OTH) AF: 0.416 AC: 878 AN: 2110

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

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