10-80195087-G-A

Variant summary

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

The NM_145868.2(ANXA11):​c.-58+10256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,022 control chromosomes in the GnomAD database, including 1,916 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 0.14 ( 1916 hom., cov: 32)

Consequence

ANXA11
NM_145868.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48
Variant links:
Genes affected
ANXA11 (HGNC:535): (annexin A11) This gene encodes a member of the annexin family, a group of calcium-dependent phospholipid-binding proteins. Annexins have unique N-terminal domains and conserved C-terminal domains, which contain calcium-dependent phospholipid-binding sites. The encoded protein is a 56-kD antigen recognized by sera from patients with various autoimmune diseases. Several transcript variants encoding two different isoforms have been identified. [provided by RefSeq, Dec 2015]

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=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANXA11NM_145868.2 linkuse as main transcriptc.-58+10256C>T intron_variant ENST00000422982.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANXA11ENST00000422982.8 linkuse as main transcriptc.-58+10256C>T intron_variant 1 NM_145868.2 P2P50995-1

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21596
AN:
151904
Hom.:
1908
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.0493
Gnomad AMR
AF:
0.0809
Gnomad ASJ
AF:
0.0827
Gnomad EAS
AF:
0.212
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.143
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0906
Gnomad OTH
AF:
0.127
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.142
AC:
21629
AN:
152022
Hom.:
1916
Cov.:
32
AF XY:
0.145
AC XY:
10784
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.238
Gnomad4 AMR
AF:
0.0808
Gnomad4 ASJ
AF:
0.0827
Gnomad4 EAS
AF:
0.212
Gnomad4 SAS
AF:
0.238
Gnomad4 FIN
AF:
0.143
Gnomad4 NFE
AF:
0.0906
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.0991
Hom.:
1684
Bravo
AF:
0.141
Asia WGS
AF:
0.227
AC:
791
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.48
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs11202059; hg19: chr10-81954843; API