chr10-80155380-T-C

Position:

• chr10-80155380-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.*473A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 156,018 control chromosomes in the GnomAD database, including 56,354 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 0.84 (54766 hom., cov: 32)
  • Exomes 𝑓: 0.90 (1588 hom.)
• Consequence: ANXA11 NM_145868.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA11	NM_145868.2	c.*473A>G		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	c.*473A>G		3_prime_UTR_variant	16/16	1	NM_145868.2	ENSP00000404412.2
ANXA11	ENST00000372231	c.*473A>G		3_prime_UTR_variant	15/15	1		ENSP00000361305.3
ANXA11	ENST00000438331	c.*473A>G		3_prime_UTR_variant	17/17	1		ENSP00000398610.1
ANXA11	ENST00000265447	c.*473A>G		3_prime_UTR_variant	15/15	5		ENSP00000265447.5

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128384 AN: 152038 Hom.: 54714 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.864

GnomAD4 exome AF: 0.905 AC: 3495 AN: 3862 Hom.: 1588 Cov.: 0 AF XY: 0.909 AC XY: 1845 AN XY: 2030

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.933

Gnomad4 ASJ exome AF: 0.776

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.960

Gnomad4 FIN exome AF: 0.914

Gnomad4 NFE exome AF: 0.892

Gnomad4 OTH exome AF: 0.920

GnomAD4 genome AF: 0.844 AC: 128488 AN: 152156 Hom.: 54766 Cov.: 32 AF XY: 0.848 AC XY: 63051 AN XY: 74394

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.866

Alfa AF: 0.880 Hom.: 77527

Bravo AF: 0.838

Asia WGS AF: 0.958 AC: 3332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.31

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: rs2789686; hg19: chr10-81915136;