rs13277433

Positions:

• chr8-123713088-G-T

Variant summary

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

The NM_004306.4(ANXA13):​c.16-335C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,208 control chromosomes in the GnomAD database, including 5,007 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 0.23 (5007 hom., cov: 32)
• Consequence: ANXA13 NM_004306.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA13	NM_004306.4	c.16-335C>A		intron_variant		ENST00000419625.6
ANXA13	NM_001003954.3	c.139-335C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANXA13	ENST00000419625.6	c.16-335C>A		intron_variant		1	NM_004306.4	P1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34640 AN: 152090 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.228 AC: 34667 AN: 152208 Hom.: 5007 Cov.: 32 AF XY: 0.234 AC XY: 17389 AN XY: 74418

Gnomad4 AFR AF: 0.0544

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.235

Alfa AF: 0.269 Hom.: 5888

Bravo AF: 0.223

Asia WGS AF: 0.333 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0060
DANN	Benign	0.54

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: rs13277433; hg19: chr8-124725328;