rs10496684

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-131603900-C-A
• chr2-131603900-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 0 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: 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397487.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POTEKP	NR_033885.3		n.594-118C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POTEKP	ENST00000397487.4	TSL:6	n.884-118C>A		intron	N/A
	ENSG00000286208	ENST00000727992.1		n.1713-118C>A		intron	N/A
	ENSG00000286208	ENST00000727993.1		n.1102-118C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000128 AC: 1 AN: 778966 Hom.: 0 AF XY: 0.00000253 AC XY: 1 AN XY: 395446

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

African (AFR) AF: 0.00 AC: 0 AN: 17540

American (AMR) AF: 0.00 AC: 0 AN: 20188

Ashkenazi Jewish (ASJ) AF: 0.0000664 AC: 1 AN: 15056

East Asian (EAS) AF: 0.00 AC: 0 AN: 23132

South Asian (SAS) AF: 0.00 AC: 0 AN: 57190

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32028

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2234

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 578674

Other (OTH) AF: 0.00 AC: 0 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.

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.16
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;