chr4-78592061-A-G

Variant summary

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

The NM_005139.3(ANXA3):​c.483+438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,982 control chromosomes in the GnomAD database, including 26,869 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 0.59 ( 26869 hom., cov: 32)

Consequence

ANXA3
NM_005139.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820
Variant links:
Genes affected
ANXA3 (HGNC:541): (annexin A3) This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. This protein functions in the inhibition of phopholipase A2 and cleavage of inositol 1,2-cyclic phosphate to form inositol 1-phosphate. This protein may also play a role in anti-coagulation. [provided by RefSeq, Jul 2008]

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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANXA3NM_005139.3 linkuse as main transcriptc.483+438A>G intron_variant ENST00000264908.11 NP_005130.1
ANXA3XM_047450154.1 linkuse as main transcriptc.483+438A>G intron_variant XP_047306110.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANXA3ENST00000264908.11 linkuse as main transcriptc.483+438A>G intron_variant 1 NM_005139.3 ENSP00000264908 P1
ANXA3ENST00000503570.6 linkuse as main transcriptc.366+438A>G intron_variant 5 ENSP00000421015
ANXA3ENST00000512542.5 linkuse as main transcriptc.16-3320A>G intron_variant 3 ENSP00000426591
ANXA3ENST00000512884.5 linkuse as main transcriptc.366+438A>G intron_variant 5 ENSP00000423068

Frequencies

GnomAD3 genomes
AF:
0.591
AC:
89730
AN:
151866
Hom.:
26864
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.505
Gnomad AMI
AF:
0.767
Gnomad AMR
AF:
0.563
Gnomad ASJ
AF:
0.643
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.547
Gnomad FIN
AF:
0.607
Gnomad MID
AF:
0.661
Gnomad NFE
AF:
0.643
Gnomad OTH
AF:
0.620
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.591
AC:
89787
AN:
151982
Hom.:
26869
Cov.:
32
AF XY:
0.587
AC XY:
43621
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.505
Gnomad4 AMR
AF:
0.563
Gnomad4 ASJ
AF:
0.643
Gnomad4 EAS
AF:
0.603
Gnomad4 SAS
AF:
0.547
Gnomad4 FIN
AF:
0.607
Gnomad4 NFE
AF:
0.643
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.631
Hom.:
63951
Bravo
AF:
0.584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.5
DANN
Benign
0.44

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: rs2867461; hg19: chr4-79513215; API