chr5-43004178-A-G

Variant names:

• chr5-43004178-A-G
• rs316414
• ENST00000771912.1:n.101-18516T>C

Variant summary

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

The ENST00000771912.1(ANXA2R-OT1):​n.101-18516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,090 control chromosomes in the GnomAD database, including 34,561 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 0.67 (34561 hom., cov: 32)
• Consequence: ANXA2R-OT1 ENST00000771912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 9 publications found

Genes affected

ANXA2R-OT1 (HGNC:48996): (ANXA2R overlapping transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANXA2R-OT1	ENST00000771912.1	n.101-18516T>C		intron_variant	Intron 2 of 4
ANXA2R-OT1	ENST00000771913.1	n.285-18516T>C		intron_variant	Intron 1 of 2
ANXA2R-OT1	ENST00000771914.1	n.145-18516T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101518 AN: 151972 Hom.: 34520 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.668 AC: 101608 AN: 152090 Hom.: 34561 Cov.: 32 AF XY: 0.661 AC XY: 49139 AN XY: 74352

African (AFR) AF: 0.745 AC: 30891 AN: 41474

American (AMR) AF: 0.545 AC: 8326 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1939 AN: 5176

South Asian (SAS) AF: 0.611 AC: 2947 AN: 4824

European-Finnish (FIN) AF: 0.640 AC: 6768 AN: 10574

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46096 AN: 67966

Other (OTH) AF: 0.674 AC: 1425 AN: 2114

Alfa AF: 0.649 Hom.: 5667

Bravo AF: 0.660

Asia WGS AF: 0.512 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.22
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs316414; hg19: chr5-43004280;