Variant 10-80157952-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_145868.2(ANXA11):c.1335+15T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 1,612,348 control chromosomes in the GnomAD database, including 206,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 15398 hom., cov: 31)

Exomes 𝑓: 0.51 ( 191164 hom. )

Consequence

ANXA11
NM_145868.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.512

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:

ANXA11 (HGNC:):

ANXA11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 10-80157952-A-G is Benign according to our data. Variant chr10-80157952-A-G is described in ClinVar as [Benign]. Clinvar id is 1244057.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA11	NM_145868.2 linkuse as main transcript	c.1335+15T>C		intron_variant		ENST00000422982.8	NP_665875.1	P50995-1Q5T0G8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8 linkuse as main transcript	c.1335+15T>C		intron_variant		1	NM_145868.2	ENSP00000404412.2		P50995-1

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65331

AN:

151860

Hom.:

15396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.475

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.584

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.449

GnomAD3 exomes

AF:

0.482

AC:

121237

AN:

251306

Hom.:

30321

AF XY:

0.481

AC XY:

65317

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.518

Gnomad ASJ exome

AF:

0.429

Gnomad EAS exome

AF:

0.574

Gnomad SAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.562

Gnomad NFE exome

AF:

0.514

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.507

AC:

740229

AN:

1460370

Hom.:

191164

Cov.:

AF XY:

0.503

AC XY:

365487

AN XY:

726640

show subpopulations

Gnomad4 AFR exome

AF:

0.209

Gnomad4 AMR exome

AF:

0.514

Gnomad4 ASJ exome

AF:

0.432

Gnomad4 EAS exome

AF:

0.589

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.562

Gnomad4 NFE exome

AF:

0.524

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.430

AC:

65339

AN:

151978

Hom.:

15398

Cov.:

AF XY:

0.432

AC XY:

32052

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.583

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.576

Gnomad4 NFE

AF:

0.519

Gnomad4 OTH

AF:

0.445

Alfa

AF:

0.497

Hom.:

26774

Bravo

AF:

0.417

Asia WGS

AF:

0.434

AC:

1506

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

-0.86

CADD

Benign

0.33

DANN

Benign

0.55

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