rs11026318

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648804.1(ANO5):​n.269+18923C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,078 control chromosomes in the GnomAD database, including 2,784 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 0.16 ( 2784 hom., cov: 32)

Consequence

ANO5
ENST00000648804.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.769
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC102723370XR_007062618.1 linkuse as main transcriptn.113+18923C>T intron_variant
LOC102723370XR_007062619.1 linkuse as main transcriptn.649+80430C>T intron_variant
LOC102723370XR_931110.3 linkuse as main transcriptn.199+80430C>T intron_variant
LOC102723370XR_931111.3 linkuse as main transcriptn.113+18923C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANO5ENST00000648804.1 linkuse as main transcriptn.269+18923C>T intron_variant
ANO5ENST00000682428.1 linkuse as main transcriptn.197-57015C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.160
AC:
24321
AN:
151960
Hom.:
2776
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.292
Gnomad AMI
AF:
0.0747
Gnomad AMR
AF:
0.247
Gnomad ASJ
AF:
0.0948
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.127
Gnomad FIN
AF:
0.120
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0728
Gnomad OTH
AF:
0.151
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.160
AC:
24377
AN:
152078
Hom.:
2784
Cov.:
32
AF XY:
0.163
AC XY:
12099
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.292
Gnomad4 AMR
AF:
0.248
Gnomad4 ASJ
AF:
0.0948
Gnomad4 EAS
AF:
0.176
Gnomad4 SAS
AF:
0.127
Gnomad4 FIN
AF:
0.120
Gnomad4 NFE
AF:
0.0728
Gnomad4 OTH
AF:
0.150
Alfa
AF:
0.0928
Hom.:
1609
Bravo
AF:
0.180
Asia WGS
AF:
0.166
AC:
580
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.11
DANN
Benign
0.23

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11026318; hg19: chr11-21896880; API