GeneBe

8-43338564-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000519951.2(POTEA):​c.1188-3315G>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
ENST00000519951.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.195

Publications

1 publications found
Variant links:
Genes affected
POTEA (HGNC:33893): (POTE ankyrin domain family member A)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
POTEANM_001005365.2 linkc.1188-3315G>A intron_variant Intron 9 of 13 NP_001005365.2 Q6S8J7-1
POTEANM_001002920.1 linkc.1050-3315G>A intron_variant Intron 8 of 12 NP_001002920.1 Q6S8J7-2
POTEAXM_024447146.1 linkc.1187+19942G>A intron_variant Intron 9 of 10 XP_024302914.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POTEAENST00000519951.2 linkc.1188-3315G>A intron_variant Intron 9 of 13 1 ENSP00000492193.1
POTEAENST00000522175.7 linkc.1050-3315G>A intron_variant Intron 8 of 12 1 ENSP00000492265.1

Frequencies

GnomAD3 genomes
AF:
0.0456
AC:
6938
AN:
152048
Hom.:
318
Cov.:
33
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.117
AC:
4844
AN:
41510
American (AMR)
AF:
0.0190
AC:
291
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.00259
AC:
9
AN:
3472
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5168
South Asian (SAS)
AF:
0.0174
AC:
84
AN:
4822
European-Finnish (FIN)
AF:
0.0361
AC:
383
AN:
10600
Middle Eastern (MID)
AF:
0.0136
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
0.0186
AC:
1266
AN:
67998
Other (OTH)
AF:
0.0322
AC:
68
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
333
667
1000
1334
1667
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
76
152
228
304
380
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0178
Hom.:
9
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
PhyloP100
-0.20
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs10504052; hg19: chr8-43193707; API