rs2819941

Positions:

• chr10-80201265-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145868.2(ANXA11):​c.-58+4078G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,920 control chromosomes in the GnomAD database, including 33,041 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (33041 hom., cov: 30)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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	Protein	UniProt
ANXA11	NM_145868.2	c.-58+4078G>A		intron_variant		ENST00000422982.8	NP_665875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8	c.-58+4078G>A		intron_variant		1	NM_145868.2	ENSP00000404412	P2

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98580 AN: 151802 Hom.: 32968 Cov.: 30

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.633

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.650 AC: 98714 AN: 151920 Hom.: 33041 Cov.: 30 AF XY: 0.645 AC XY: 47843 AN XY: 74224

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.635

Alfa AF: 0.612 Hom.: 54788

Bravo AF: 0.657

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs2819941; hg19: chr10-81961021; COSMIC: COSV55415815;