rs1050606

Variant summary

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

The NM_001154.4(ANXA5):​c.-64T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 294,552 control chromosomes in the GnomAD database, including 35,812 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 0.50 ( 19448 hom., cov: 33)
Exomes 𝑓: 0.47 ( 16364 hom. )

Consequence

ANXA5
NM_001154.4 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.563
Variant links:
Genes affected
ANXA5 (HGNC:543): (annexin A5) The Annexin 5 gene spans 29 kb containing 13 exons, and encodes a single transcript of approximately 1.6 kb and a protein product with a molecular weight of about 35 kDa.The protein encoded by this gene belongs to the annexin family of calcium-dependent phospholipid binding proteins some of which have been implicated in membrane-related events along exocytotic and endocytotic pathways. Annexin 5 is a phospholipase A2 and protein kinase C inhibitory protein with calcium channel activity and a potential role in cellular signal transduction, inflammation, growth and differentiation. Annexin 5 has also been described as placental anticoagulant protein I, vascular anticoagulant-alpha, endonexin II, lipocortin V, placental protein 4 and anchorin CII. Polymorphisms in this gene have been implicated in various obstetric complications. [provided by RefSeq, Dec 2019]

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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 (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANXA5NM_001154.4 linkuse as main transcriptc.-64T>G 5_prime_UTR_variant 1/13 ENST00000296511.10 NP_001145.1 P08758V9HWE0
ANXA5XM_017008141.3 linkuse as main transcriptc.-64T>G 5_prime_UTR_variant 1/7 XP_016863630.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANXA5ENST00000296511.10 linkuse as main transcriptc.-64T>G 5_prime_UTR_variant 1/131 NM_001154.4 ENSP00000296511.5 P08758

Frequencies

GnomAD3 genomes
AF:
0.500
AC:
76012
AN:
151944
Hom.:
19439
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.561
Gnomad AMI
AF:
0.615
Gnomad AMR
AF:
0.463
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.269
Gnomad SAS
AF:
0.401
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.511
Gnomad OTH
AF:
0.499
GnomAD4 exome
AF:
0.474
AC:
67592
AN:
142492
Hom.:
16364
Cov.:
1
AF XY:
0.476
AC XY:
34324
AN XY:
72116
show subpopulations
Gnomad4 AFR exome
AF:
0.552
Gnomad4 AMR exome
AF:
0.449
Gnomad4 ASJ exome
AF:
0.446
Gnomad4 EAS exome
AF:
0.209
Gnomad4 SAS exome
AF:
0.404
Gnomad4 FIN exome
AF:
0.430
Gnomad4 NFE exome
AF:
0.516
Gnomad4 OTH exome
AF:
0.487
GnomAD4 genome
AF:
0.500
AC:
76056
AN:
152060
Hom.:
19448
Cov.:
33
AF XY:
0.491
AC XY:
36499
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.560
Gnomad4 AMR
AF:
0.462
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.269
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.413
Gnomad4 NFE
AF:
0.511
Gnomad4 OTH
AF:
0.492
Alfa
AF:
0.508
Hom.:
2405
Bravo
AF:
0.508
Asia WGS
AF:
0.357
AC:
1244
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
7.5
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1050606; hg19: chr4-122618046; API