rs12256429

chr10-80178876-T-C

Variant summary

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

The NM_145868.2(ANXA11):c.-57-2721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,122 control chromosomes in the GnomAD database, including 1,399 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 0.13 (1399 hom., cov: 32)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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 (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA11	NM_145868.2	c.-57-2721A>G		intron_variant		ENST00000422982.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA11	ENST00000422982.8	c.-57-2721A>G		intron_variant		1	NM_145868.2	P2
ANXA11	ENST00000372231.7	c.-8-6007A>G		intron_variant		1		P2
ANXA11	ENST00000438331.5	c.-58+2065A>G		intron_variant		1		P2
ANXA11	ENST00000463657.1	n.695+2065A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19573 AN: 152004 Hom.: 1393 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.129 AC: 19602 AN: 152122 Hom.: 1399 Cov.: 32 AF XY: 0.131 AC XY: 9706 AN XY: 74360

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0175

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.146

Alfa AF: 0.144 Hom.: 281

Bravo AF: 0.136

Asia WGS AF: 0.147 AC: 510 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	3.8
Dann	Benign	0.72

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: rs12256429; hg19: chr10-81938632;