10-80173034-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.-8-165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 605,178 control chromosomes in the GnomAD database, including 107,947 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.63 (31589 hom., cov: 34)
  • Exomes 𝑓: 0.57 (76358 hom.)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0820

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=-0.85).
• BP6: Variant 10-80173034-T-C is Benign according to our data. Variant chr10-80173034-T-C is described in ClinVar as [Benign]. Clinvar id is 1231246.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA11	NM_145868.2	c.-8-165A>G		intron_variant		ENST00000422982.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA11	ENST00000422982.8	c.-8-165A>G		intron_variant		1	NM_145868.2	P2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96207 AN: 152058 Hom.: 31514 Cov.: 34

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.574 AC: 260165 AN: 453002 Hom.: 76358 Cov.: 5 AF XY: 0.576 AC XY: 137554 AN XY: 238676

Gnomad4 AFR exome AF: 0.796

Gnomad4 AMR exome AF: 0.554

Gnomad4 ASJ exome AF: 0.618

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.632

Gnomad4 FIN exome AF: 0.542

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.585

GnomAD4 genome AF: 0.633 AC: 96340 AN: 152176 Hom.: 31589 Cov.: 34 AF XY: 0.629 AC XY: 46818 AN XY: 74392

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.615

Alfa AF: 0.625 Hom.: 3738

Bravo AF: 0.641

Asia WGS AF: 0.560 AC: 1949 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	-0.85
Cadd	Benign	3.2
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs2236556; hg19: chr10-81932790;