Genetic Variant ANXA2P3:n.977A>C (chr10-64826548-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000404883.2(ANXA2P3):n.977A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA2P3	NR_001446.2 link	n.1021A>C		non_coding_transcript_exon_variant	Exon 1 of 1
LOC105378336	XR_946020.2 link	n.49+11546A>C		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>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293732	ENST00000718642.1 link	n.195+11546A>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

575324

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

315622

African (AFR)

AF:

0.00

AC:

AN:

16390

American (AMR)

AF:

0.00

AC:

AN:

41800

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19246

East Asian (EAS)

AF:

0.00

AC:

AN:

32926

South Asian (SAS)

AF:

0.00

AC:

AN:

68854

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42060

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3908

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

320444

Other (OTH)

AF:

0.00

AC:

AN:

29696

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.1

(source)

DANN

Benign

0.35

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over