rs2789695

Positions:

• chr10-80187084-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.-57-10929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,108 control chromosomes in the GnomAD database, including 31,504 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 0.63 (31504 hom., cov: 33)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA11	NM_145868.2	c.-57-10929G>A		intron_variant		ENST00000422982.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA11	ENST00000422982.8	c.-57-10929G>A		intron_variant		1	NM_145868.2	P2

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96079 AN: 151990 Hom.: 31429 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.633 AC: 96212 AN: 152108 Hom.: 31504 Cov.: 33 AF XY: 0.629 AC XY: 46758 AN XY: 74340

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.617

Alfa AF: 0.604 Hom.: 12604

Bravo AF: 0.641

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.58

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: rs2789695; hg19: chr10-81946840;