rs13258681

Positions:

• chr8-123702482-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004306.4(ANXA13):​c.186+160A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,168 control chromosomes in the GnomAD database, including 5,653 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 0.27 (5653 hom., cov: 32)
• Consequence: ANXA13 NM_004306.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

ANXA13 (HGNC:536): (annexin A13) This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. The specific function of this gene has not yet been determined; however, it is associated with the plasma membrane of undifferentiated, proliferating endothelial cells and differentiated villus enterocytes. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA13	NM_004306.4	c.186+160A>G		intron_variant		ENST00000419625.6
ANXA13	NM_001003954.3	c.309+160A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA13	ENST00000419625.6	c.186+160A>G		intron_variant		1	NM_004306.4	P1
ANXA13	ENST00000262219.10	c.309+160A>G		intron_variant		1
ANXA13	ENST00000520519.1	c.99+160A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40603 AN: 152050 Hom.: 5656 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.267 AC: 40611 AN: 152168 Hom.: 5653 Cov.: 32 AF XY: 0.262 AC XY: 19524 AN XY: 74392

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.283

Alfa AF: 0.294 Hom.: 5644

Bravo AF: 0.260

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	8.2
DANN	Benign	0.85

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: rs13258681; hg19: chr8-124714722; COSMIC: COSV51621398;