rs61860052

Positions:

• chr10-80201955-C-A
• chr10-80201955-C-G
• chr10-80201955-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.-58+3388G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 152,218 control chromosomes in the GnomAD database, including 457 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 0.064 (457 hom., cov: 31)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.09 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA11	NM_145868.2	c.-58+3388G>T		intron_variant		ENST00000422982.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA11	ENST00000422982.8	c.-58+3388G>T		intron_variant		1	NM_145868.2	P2

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9705 AN: 152100 Hom.: 457 Cov.: 31

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0638 AC: 9707 AN: 152218 Hom.: 457 Cov.: 31 AF XY: 0.0631 AC XY: 4695 AN XY: 74428

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0919

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0473 Hom.: 47

Bravo AF: 0.0616

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
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: rs61860052; hg19: chr10-81961711;