Variant 10-80157564-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_145868.2(ANXA11):c.1458+77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,564,900 control chromosomes in the GnomAD database, including 1,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.025 ( 56 hom., cov: 32)

Exomes 𝑓: 0.038 ( 1163 hom. )

Consequence

ANXA11
NM_145868.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0620

Variant links:

Genes affected

ANXA11 (HGNC:535): (annexin A11) This gene encodes a member of the annexin family, a group of calcium-dependent phospholipid-binding proteins. Annexins have unique N-terminal domains and conserved C-terminal domains, which contain calcium-dependent phospholipid-binding sites. The encoded protein is a 56-kD antigen recognized by sera from patients with various autoimmune diseases. Several transcript variants encoding two different isoforms have been identified. [provided by RefSeq, Dec 2015]

ANXA11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 10-80157564-G-A is Benign according to our data. Variant chr10-80157564-G-A is described in ClinVar as [Benign]. Clinvar id is 1693167.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0252 (3834/152208) while in subpopulation NFE AF= 0.0391 (2656/68006). AF 95% confidence interval is 0.0378. There are 56 homozygotes in gnomad4. There are 1846 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3834 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA11	NM_145868.2 linkuse as main transcript	c.1458+77C>T		intron_variant		ENST00000422982.8	NP_665875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8 linkuse as main transcript	c.1458+77C>T		intron_variant		1	NM_145868.2	ENSP00000404412	P2	P50995-1

Frequencies

GnomAD3 genomes

AF:

0.0252

AC:

3836

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00662

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0162

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0381

Gnomad FIN

AF:

0.0268

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0391

Gnomad OTH

AF:

0.0225

GnomAD4 exome

AF:

0.0379

AC:

53517

AN:

1412692

Hom.:

1163

Cov.:

AF XY:

0.0381

AC XY:

26511

AN XY:

696542

show subpopulations

Gnomad4 AFR exome

AF:

0.00569

Gnomad4 AMR exome

AF:

0.0150

Gnomad4 ASJ exome

AF:

0.0341

Gnomad4 EAS exome

AF:

0.000102

Gnomad4 SAS exome

AF:

0.0406

Gnomad4 FIN exome

AF:

0.0298

Gnomad4 NFE exome

AF:

0.0414

Gnomad4 OTH exome

AF:

0.0349

GnomAD4 genome

AF:

0.0252

AC:

3834

AN:

152208

Hom.:

Cov.:

AF XY:

0.0248

AC XY:

1846

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00660

Gnomad4 AMR

AF:

0.0162

Gnomad4 ASJ

AF:

0.0323

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0382

Gnomad4 FIN

AF:

0.0268

Gnomad4 NFE

AF:

0.0391

Gnomad4 OTH

AF:

0.0223

Alfa

AF:

0.0318

Hom.:

Bravo

AF:

0.0248

Asia WGS

AF:

0.0150

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Inclusion body myopathy and brain white matter abnormalities

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.4

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over