rs3758354

Variant names:

• chr9-73149649-A-C
• rs3758354
• ENST00000954795.1:c.-43A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-73149649-A-C
• chr9-73149649-A-G

Variant summary

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

The ENST00000954795.1(ANXA1):​c.-43A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,140 control chromosomes in the GnomAD database, including 509 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 0.074 (509 hom., cov: 32)
• Consequence: ANXA1 ENST00000954795.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 16 publications found

Genes affected

ANXA1 (HGNC:533): (annexin A1) This gene encodes a membrane-localized protein that binds phospholipids. This protein inhibits phospholipase A2 and has anti-inflammatory activity. Loss of function or expression of this gene has been detected in multiple tumors. [provided by RefSeq, Dec 2014]

ENSG00000293607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000954795.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANXA1	ENST00000954795.1		c.-43A>C		5_prime_UTR	Exon 2 of 14	ENSP00000624854.1
	ANXA1	ENST00000954796.1		c.-43A>C		5_prime_UTR	Exon 1 of 13	ENSP00000624855.1
	ENSG00000293607	ENST00000715863.1		n.263-37743T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0737 AC: 11201 AN: 152022 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0736 AC: 11204 AN: 152140 Hom.: 509 Cov.: 32 AF XY: 0.0727 AC XY: 5405 AN XY: 74360

African (AFR) AF: 0.137 AC: 5668 AN: 41508

American (AMR) AF: 0.0548 AC: 837 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.163 AC: 843 AN: 5170

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4810

European-Finnish (FIN) AF: 0.0322 AC: 341 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2809 AN: 67972

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0562 Hom.: 1247

Bravo AF: 0.0816

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3758354; hg19: chr9-75764565;