Variant chr10-80162162-T-C 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.1087-134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 662,152 control chromosomes in the GnomAD database, including 59,076 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11394 hom., cov: 34)

Exomes 𝑓: 0.42 ( 47682 hom. )

Consequence

ANXA11
NM_145868.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.110

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-80162162-T-C is Benign according to our data. Variant chr10-80162162-T-C is described in ClinVar as [Benign]. Clinvar id is 1281123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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.1087-134A>G		intron_variant		ENST00000422982.8	NP_665875.1	P50995-1Q5T0G8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ANXA11	ENST00000422982.8 linkuse as main transcript	c.1087-134A>G	intron_variant	1	NM_145868.2	ENSP00000404412.2	P50995-1
ANXA11	ENST00000372231.7 linkuse as main transcript	c.1087-134A>G	intron_variant	1		ENSP00000361305.3	P50995-1
ANXA11	ENST00000438331.5 linkuse as main transcript	c.1087-134A>G	intron_variant	1		ENSP00000398610.1	P50995-1
ANXA11	ENST00000265447.8 linkuse as main transcript	c.988-134A>G	intron_variant	5		ENSP00000265447.5	P50995-2

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56114

AN:

152048

Hom.:

11392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.388

GnomAD4 exome

AF:

0.421

AC:

214761

AN:

509986

Hom.:

47682

AF XY:

0.419

AC XY:

111405

AN XY:

265788

show subpopulations

Gnomad4 AFR exome

AF:

0.201

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.378

Gnomad4 EAS exome

AF:

0.651

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.455

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.412

GnomAD4 genome

AF:

0.369

AC:

56106

AN:

152166

Hom.:

11394

Cov.:

AF XY:

0.372

AC XY:

27699

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.671

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.453

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.398

Hom.:

5785

Bravo

AF:

0.361

Asia WGS

AF:

0.458

AC:

1589

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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