dbSNP rs10496684: POTEKP:n.884-118C>A (chr2-131603900-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000397487.4(POTEKP):n.884-118C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000128 in 778,966 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 34)

Exomes 𝑓: 0.0000013 ( 0 hom. )

Consequence

POTEKP
ENST00000397487.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.736

Publications

0 publications found

Variant links:

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]

POTEKP links:

ENSG00000286208 (HGNC:):

ENSG00000286208 links:

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ACMG classification

Classification was made for transcript

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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POTEKP	NR_033885.3 link	n.594-118C>A		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
POTEKP	ENST00000397487.4 link	n.884-118C>A	intron_variant	Intron 5 of 10	6
ENSG00000286208	ENST00000727992.1 link	n.1713-118C>A	intron_variant	Intron 11 of 13
ENSG00000286208	ENST00000727993.1 link	n.1102-118C>A	intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000128

AC:

AN:

778966

Hom.:

AF XY:

0.00000253

AC XY:

AN XY:

395446

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

17540

American (AMR)

AF:

0.00

AC:

AN:

20188

Ashkenazi Jewish (ASJ)

AF:

0.0000664

AC:

AN:

15056

East Asian (EAS)

AF:

0.00

AC:

AN:

23132

South Asian (SAS)

AF:

0.00

AC:

AN:

57190

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32028

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2234

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

578674

Other (OTH)

AF:

0.00

AC:

AN:

32924

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.28

(source)

DANN

Benign

0.16

PhyloP100

-0.74

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over