5-151137464-C-G

Variant names:

• chr5-151137464-C-G
• rs9324679
• NM_001155.5:c.319-143G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001155.5(ANXA6):​c.319-143G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 541,344 control chromosomes in the GnomAD database, including 141,401 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 0.73 (40405 hom., cov: 30)
  • Exomes 𝑓: 0.71 (100996 hom.)
• Consequence: ANXA6 NM_001155.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 1 publications found

Genes affected

ANXA6 (HGNC:544): (annexin A6) Annexin VI belongs to a family of calcium-dependent membrane and phospholipid binding proteins. Several members of the annexin family have been implicated in membrane-related events along exocytotic and endocytotic pathways. The annexin VI gene is approximately 60 kbp long and contains 26 exons. It encodes a protein of about 68 kDa that consists of eight 68-amino acid repeats separated by linking sequences of variable lengths. It is highly similar to human annexins I and II sequences, each of which contain four such repeats. Annexin VI has been implicated in mediating the endosome aggregation and vesicle fusion in secreting epithelia during exocytosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Aug 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001155.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA6	NM_001155.5	MANE Select	c.319-143G>C		intron	N/A	NP_001146.2
	ANXA6	NM_001363114.2		c.319-143G>C		intron	N/A	NP_001350043.1
	ANXA6	NM_001193544.2		c.223-143G>C		intron	N/A	NP_001180473.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA6	ENST00000354546.10	TSL:1 MANE Select	c.319-143G>C		intron	N/A	ENSP00000346550.5
	ANXA6	ENST00000517677.5	TSL:5	n.319-143G>C		intron	N/A	ENSP00000430826.1
	ANXA6	ENST00000700367.1		c.319-143G>C		intron	N/A	ENSP00000514965.1

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110345 AN: 151894 Hom.: 40352 Cov.: 30

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.708

GnomAD4 exome AF: 0.714 AC: 277969 AN: 389332 Hom.: 100996 AF XY: 0.720 AC XY: 147397 AN XY: 204786

African (AFR) AF: 0.770 AC: 8170 AN: 10606

American (AMR) AF: 0.758 AC: 11297 AN: 14910

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 7161 AN: 11914

East Asian (EAS) AF: 0.876 AC: 23785 AN: 27160

South Asian (SAS) AF: 0.863 AC: 30196 AN: 34980

European-Finnish (FIN) AF: 0.686 AC: 19358 AN: 28208

Middle Eastern (MID) AF: 0.625 AC: 1081 AN: 1730

European-Non Finnish (NFE) AF: 0.679 AC: 160844 AN: 237030

Other (OTH) AF: 0.705 AC: 16077 AN: 22794

GnomAD4 genome AF: 0.727 AC: 110454 AN: 152012 Hom.: 40405 Cov.: 30 AF XY: 0.730 AC XY: 54215 AN XY: 74290

African (AFR) AF: 0.779 AC: 32282 AN: 41454

American (AMR) AF: 0.738 AC: 11279 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2076 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4518 AN: 5170

South Asian (SAS) AF: 0.868 AC: 4175 AN: 4812

European-Finnish (FIN) AF: 0.690 AC: 7285 AN: 10554

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46448 AN: 67960

Other (OTH) AF: 0.711 AC: 1500 AN: 2110

Alfa AF: 0.687 Hom.: 4498

Bravo AF: 0.731

Asia WGS AF: 0.862 AC: 2999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9324679; hg19: chr5-150517025; COSMIC: COSV62906014; COSMIC: COSV62906014;