rs10504052

chr8-43338564-G-Achr8-43338564-G-T

Variant summary

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

The XM_024447146.1(POTEA):c.1187+19942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 152,168 control chromosomes in the GnomAD database, including 319 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 0.046 (319 hom., cov: 33)
• Consequence: POTEA XM_024447146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

POTEA (HGNC:33893): (POTE ankyrin domain family member A)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POTEA	XM_024447146.1	c.1187+19942G>A		intron_variant
POTEA	NM_001002920.1	c.1050-3315G>A		intron_variant
POTEA	NM_001005365.2	c.1188-3315G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POTEA	ENST00000519951.2	c.1188-3315G>A		intron_variant		1		P5
POTEA	ENST00000522175.7	c.1050-3315G>A		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.0456 AC: 6938 AN: 152048 Hom.: 318 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0457 AC: 6956 AN: 152168 Hom.: 319 Cov.: 33 AF XY: 0.0459 AC XY: 3418 AN XY: 74400

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0190

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0141 Hom.: 6

Bravo AF: 0.0468

Asia WGS AF: 0.0150 AC: 52 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.44
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504052; hg19: chr8-43193707;