Variant chr10-73388358-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001156.5(ANXA7):c.492T>C(p.Asp164=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0826 in 1,613,460 control chromosomes in the GnomAD database, including 8,292 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 0.10 ( 1201 hom., cov: 32)

Exomes 𝑓: 0.080 ( 7091 hom. )

Consequence

ANXA7
NM_001156.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.79

Variant links:

Genes affected

ANXA7 (HGNC:545): (annexin A7) Annexin VII is a member of the annexin family of calcium-dependent phospholipid binding proteins.The Annexin VII gene contains 14 exons and spans approximately 34 kb of DNA. An alternatively spliced cassette exon results in two mRNA transcripts of 2.0 and 2.4 kb which are predicted to generate two protein isoforms differing in their N-terminal domain. The alternative splicing event is tissue specific and the mRNA containing the cassette exon is prevalent in brain, heart and skeletal muscle. The transcripts also differ in their 3'-non coding regions by the use of two alternative poly(A) signals. Annexin VII encodes a protein with a molecular weight of approximately 51 kDa with a unique, highly hydrophobic N-terminal domain of 167 amino acids and a conserved C-terminal region of 299 amino acids. The latter domain is composed of alternating hydrophobic and hydrophilic segments. Structural analysis of the protein suggests that Annexin VII is a membrane binding protein with diverse properties, including voltage-sensitive calcium channel activity, ion selectivity and membrane fusion. [provided by RefSeq, Jul 2008]

ANXA7 links:

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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=-0.51).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA7	NM_001156.5 linkuse as main transcript	c.492T>C	p.Asp164=	synonymous_variant	6/13	ENST00000372921.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA7	ENST00000372921.10 linkuse as main transcript	c.492T>C	p.Asp164=	synonymous_variant	6/13	1	NM_001156.5	P2	P20073-2
ANXA7	ENST00000372919.8 linkuse as main transcript	c.558T>C	p.Asp186=	synonymous_variant	7/14	1		A2	P20073-1
ANXA7	ENST00000492380.1 linkuse as main transcript	n.503T>C		non_coding_transcript_exon_variant	5/8	5

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15845

AN:

152100

Hom.:

1181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0844

Gnomad ASJ

AF:

0.0987

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.0436

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0603

Gnomad OTH

AF:

0.0936

GnomAD3 exomes

AF:

0.109

AC:

27377

AN:

251356

Hom.:

2320

AF XY:

0.112

AC XY:

15197

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.162

Gnomad AMR exome

AF:

0.0851

Gnomad ASJ exome

AF:

0.106

Gnomad EAS exome

AF:

0.301

Gnomad SAS exome

AF:

0.221

Gnomad FIN exome

AF:

0.0453

Gnomad NFE exome

AF:

0.0609

Gnomad OTH exome

AF:

0.0840

GnomAD4 exome

AF:

0.0804

AC:

117422

AN:

1461242

Hom.:

7091

Cov.:

AF XY:

0.0841

AC XY:

61150

AN XY:

726902

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.0854

Gnomad4 ASJ exome

AF:

0.103

Gnomad4 EAS exome

AF:

0.285

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.0467

Gnomad4 NFE exome

AF:

0.0602

Gnomad4 OTH exome

AF:

0.0923

GnomAD4 genome

AF:

0.105

AC:

15915

AN:

152218

Hom.:

1201

Cov.:

AF XY:

0.107

AC XY:

7962

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.163

Gnomad4 AMR

AF:

0.0844

Gnomad4 ASJ

AF:

0.0987

Gnomad4 EAS

AF:

0.299

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.0436

Gnomad4 NFE

AF:

0.0603

Gnomad4 OTH

AF:

0.0964

Alfa

AF:

0.0725

Hom.:

601

Bravo

AF:

0.108

Asia WGS

AF:

0.254

AC:

883

AN:

3478

EpiCase

AF:

0.0590

EpiControl

AF:

0.0587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

9.8

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over