Genetic Variant ENST00000404883.2:n.977A>G (chr10-64826548-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000404883.2(ANXA2P3):n.977A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 726,584 control chromosomes in the GnomAD database, including 150,368 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 0.67 ( 35119 hom., cov: 32)

Exomes 𝑓: 0.63 ( 115249 hom. )

Consequence

ANXA2P3
ENST00000404883.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.34

Publications

5 publications found

Variant links:

Genes affected

ANXA2P3 (HGNC:540): (annexin A2 pseudogene 3)

ANXA2P3 links:

ENSG00000293732 (HGNC:):

ENSG00000293732 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA2P3	NR_001446.2 link	n.1021A>G		non_coding_transcript_exon_variant	Exon 1 of 1
LOC105378336	XR_946020.2 link	n.49+11546A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA2P3	ENST00000404883.2 link	n.977A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293732	ENST00000718642.1 link	n.195+11546A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.674

AC:

102459

AN:

151920

Hom.:

35073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.801

Gnomad AMI

AF:

0.779

Gnomad AMR

AF:

0.693

Gnomad ASJ

AF:

0.622

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.639

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.660

GnomAD4 exome

AF:

0.632

AC:

362984

AN:

574546

Hom.:

115249

Cov.:

AF XY:

0.630

AC XY:

198719

AN XY:

315232

show subpopulations

African (AFR)

AF:

0.801

AC:

13112

AN:

16376

American (AMR)

AF:

0.687

AC:

28707

AN:

41780

Ashkenazi Jewish (ASJ)

AF:

0.604

AC:

11602

AN:

19224

East Asian (EAS)

AF:

0.579

AC:

19027

AN:

32848

South Asian (SAS)

AF:

0.650

AC:

44756

AN:

68838

European-Finnish (FIN)

AF:

0.607

AC:

25489

AN:

41974

Middle Eastern (MID)

AF:

0.625

AC:

2440

AN:

3904

European-Non Finnish (NFE)

AF:

0.622

AC:

198973

AN:

319942

Other (OTH)

AF:

0.636

AC:

18878

AN:

29660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

7723

15446

23169

30892

38615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1166

2332

3498

4664

5830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.675

AC:

102560

AN:

152038

Hom.:

35119

Cov.:

AF XY:

0.672

AC XY:

49893

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.801

AC:

33253

AN:

41508

American (AMR)

AF:

0.693

AC:

10576

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.622

AC:

2157

AN:

3468

East Asian (EAS)

AF:

0.596

AC:

3066

AN:

5144

South Asian (SAS)

AF:

0.640

AC:

3086

AN:

4822

European-Finnish (FIN)

AF:

0.588

AC:

6199

AN:

10548

Middle Eastern (MID)

AF:

0.606

AC:

177

AN:

292

European-Non Finnish (NFE)

AF:

0.617

AC:

41953

AN:

67978

Other (OTH)

AF:

0.657

AC:

1386

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1700

3399

5099

6798

8498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.636

Hom.:

39163

Bravo

AF:

0.688

Asia WGS

AF:

0.636

AC:

2217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.5

(source)

DANN

Benign

0.39

PhyloP100

2.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over