10-80157564-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_145868.2(ANXA11):​c.1458+77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,564,900 control chromosomes in the GnomAD database, including 1,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.025 ( 56 hom., cov: 32)
Exomes 𝑓: 0.038 ( 1163 hom. )

Consequence

ANXA11
NM_145868.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0620
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 10-80157564-G-A is Benign according to our data. Variant chr10-80157564-G-A is described in ClinVar as [Benign]. Clinvar id is 1693167.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0252 (3834/152208) while in subpopulation NFE AF= 0.0391 (2656/68006). AF 95% confidence interval is 0.0378. There are 56 homozygotes in gnomad4. There are 1846 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3834 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANXA11NM_145868.2 linkuse as main transcriptc.1458+77C>T intron_variant ENST00000422982.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANXA11ENST00000422982.8 linkuse as main transcriptc.1458+77C>T intron_variant 1 NM_145868.2 P2P50995-1

Frequencies

GnomAD3 genomes
AF:
0.0252
AC:
3836
AN:
152090
Hom.:
56
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00662
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.0162
Gnomad ASJ
AF:
0.0323
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0381
Gnomad FIN
AF:
0.0268
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0391
Gnomad OTH
AF:
0.0225
GnomAD4 exome
AF:
0.0379
AC:
53517
AN:
1412692
Hom.:
1163
Cov.:
31
AF XY:
0.0381
AC XY:
26511
AN XY:
696542
show subpopulations
Gnomad4 AFR exome
AF:
0.00569
Gnomad4 AMR exome
AF:
0.0150
Gnomad4 ASJ exome
AF:
0.0341
Gnomad4 EAS exome
AF:
0.000102
Gnomad4 SAS exome
AF:
0.0406
Gnomad4 FIN exome
AF:
0.0298
Gnomad4 NFE exome
AF:
0.0414
Gnomad4 OTH exome
AF:
0.0349
GnomAD4 genome
AF:
0.0252
AC:
3834
AN:
152208
Hom.:
56
Cov.:
32
AF XY:
0.0248
AC XY:
1846
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.00660
Gnomad4 AMR
AF:
0.0162
Gnomad4 ASJ
AF:
0.0323
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0382
Gnomad4 FIN
AF:
0.0268
Gnomad4 NFE
AF:
0.0391
Gnomad4 OTH
AF:
0.0223
Alfa
AF:
0.0318
Hom.:
13
Bravo
AF:
0.0248
Asia WGS
AF:
0.0150
AC:
52
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inclusion body myopathy and brain white matter abnormalities Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabDec 05, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.4
DANN
Benign
0.65
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs12775374; hg19: chr10-81917320; API