chr10-80164489-G-A

Position:

• chr10-80164489-G-A

Variant summary

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

The NM_145868.2(ANXA11):​c.859-346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,972 control chromosomes in the GnomAD database, including 13,965 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 0.42 (13965 hom., cov: 33)
• Consequence: ANXA11 NM_145868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA11	NM_145868.2	c.859-346C>T		intron_variant		ENST00000422982.8	NP_665875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA11	ENST00000422982.8	c.859-346C>T		intron_variant		1	NM_145868.2	ENSP00000404412	P2
ANXA11	ENST00000372231.7	c.859-346C>T		intron_variant		1		ENSP00000361305	P2
ANXA11	ENST00000438331.5	c.859-346C>T		intron_variant		1		ENSP00000398610	P2
ANXA11	ENST00000265447.8	c.760-346C>T		intron_variant		5		ENSP00000265447	A2

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63657 AN: 151854 Hom.: 13937 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.419 AC: 63734 AN: 151972 Hom.: 13965 Cov.: 33 AF XY: 0.416 AC XY: 30872 AN XY: 74270

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.415

Alfa AF: 0.390 Hom.: 6685

Bravo AF: 0.420

Asia WGS AF: 0.363 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.66

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: rs7067644; hg19: chr10-81924245;