10-80171685-C-T

Variant names:

• chr10-80171685-C-T
• rs2573351
• NM_145868.2:c.56-770G>A

Variant summary

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

The NM_001278409.2(ANXA11):​c.-117G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 985,278 control chromosomes in the GnomAD database, including 101,753 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 0.49 (18874 hom., cov: 33)
  • Exomes 𝑓: 0.44 (82879 hom.)
• Consequence: ANXA11 NM_001278409.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANXA11	NM_145868.2	c.56-770G>A		intron_variant	Intron 3 of 15	ENST00000422982.8	NP_665875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8	c.56-770G>A		intron_variant	Intron 3 of 15	1	NM_145868.2	ENSP00000404412.2

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73840 AN: 152018 Hom.: 18835 Cov.: 33

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.444 AC: 369929 AN: 833142 Hom.: 82879 Cov.: 32 AF XY: 0.445 AC XY: 171045 AN XY: 384746

Gnomad4 AFR exome AF: 0.651

Gnomad4 AMR exome AF: 0.299

Gnomad4 ASJ exome AF: 0.507

Gnomad4 EAS exome AF: 0.312

Gnomad4 SAS exome AF: 0.418

Gnomad4 FIN exome AF: 0.447

Gnomad4 NFE exome AF: 0.440

Gnomad4 OTH exome AF: 0.453

GnomAD4 genome AF: 0.486 AC: 73930 AN: 152136 Hom.: 18874 Cov.: 33 AF XY: 0.481 AC XY: 35791 AN XY: 74376

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.457

Alfa AF: 0.461 Hom.: 3923

Bravo AF: 0.484

Asia WGS AF: 0.405 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.2
DANN	Benign	0.74

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: rs2573351; hg19: chr10-81931441;