rs2245168

chr10-80162162-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.110

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	UniProt
ANXA11	NM_145868.2	c.1087-134A>G		intron_variant		ENST00000422982.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA11	ENST00000422982.8	c.1087-134A>G		intron_variant		1	NM_145868.2	P2
ANXA11	ENST00000372231.7	c.1087-134A>G		intron_variant		1		P2
ANXA11	ENST00000438331.5	c.1087-134A>G		intron_variant		1		P2
ANXA11	ENST00000265447.8	c.988-134A>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56114 AN: 152048 Hom.: 11392 Cov.: 34

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

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.: 34 AF XY: 0.372 AC XY: 27699 AN XY: 74390

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

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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

Other links and lift over

dbSNP: rs2245168; hg19: chr10-81921918; COSMIC: COSV55417350; COSMIC: COSV55417350;