rs4970988

Positions:

• chr1-150977586-G-A
• chr1-150977586-G-T

Variant summary

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

The XM_047431989.1(ANXA9):​c.-2352G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,150 control chromosomes in the GnomAD database, including 8,435 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 0.31 (8435 hom., cov: 32)
• Consequence: ANXA9 XM_047431989.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765

Genes affected

ANXA9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANXA9	XM_047431989.1	c.-2352G>A		5_prime_UTR_variant	1/15		XP_047287945.1
ANXA9	XM_047431991.1			upstream_gene_variant			XP_047287947.1
ANXA9	XM_047431997.1			upstream_gene_variant			XP_047287953.1
ANXA9	XM_047431999.1			upstream_gene_variant			XP_047287955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46752 AN: 152032 Hom.: 8430 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.307 AC: 46760 AN: 152150 Hom.: 8435 Cov.: 32 AF XY: 0.315 AC XY: 23454 AN XY: 74364

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.329

Alfa AF: 0.249 Hom.: 1070

Bravo AF: 0.307

Asia WGS AF: 0.412 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970988; hg19: chr1-150950062;