rs7091565

Positions:

• chr10-80153805-C-T

Variant summary

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

The ENST00000422982.8(ANXA11):​c.*2048G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,126 control chromosomes in the GnomAD database, including 17,431 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 0.48 (17430 hom., cov: 33)
  • Exomes 𝑓: 0.39 (1 hom.)
• Consequence: ANXA11 ENST00000422982.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA11	NM_145868.2	c.*2048G>A		3_prime_UTR_variant	16/16	ENST00000422982.8	NP_665875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8	c.*2048G>A		3_prime_UTR_variant	16/16	1	NM_145868.2	ENSP00000404412	P2
ANXA11	ENST00000372231.7	c.*2048G>A		3_prime_UTR_variant	15/15	1		ENSP00000361305	P2
ANXA11	ENST00000438331.5	c.*2048G>A		3_prime_UTR_variant	17/17	1		ENSP00000398610	P2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72312 AN: 151980 Hom.: 17385 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.393 AC: 11 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.313 AC XY: 5 AN XY: 16

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.318

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.476 AC: 72415 AN: 152098 Hom.: 17430 Cov.: 33 AF XY: 0.476 AC XY: 35390 AN XY: 74352

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.471

Alfa AF: 0.449 Hom.: 26286

Bravo AF: 0.481

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.46

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: rs7091565; hg19: chr10-81913561; COSMIC: COSV55417897; COSMIC: COSV55417897;