rs267734

chr1-150979001-T-C

Variant summary

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

The XM_047431989.1(ANXA9):c.-937T>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 0.142 in 151,706 control chromosomes in the GnomAD database, including 2,004 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 0.14 (2004 hom., cov: 30)
• Consequence: ANXA9 XM_047431989.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

Genes affected

ANXA9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA9	XM_047431989.1	c.-937T>C		5_prime_UTR_variant	1/15
ANXA9	XM_047431991.1	c.-1098T>C		5_prime_UTR_variant	1/16
ANXA9	XM_047431997.1	c.-1033T>C		5_prime_UTR_variant	1/16
ANXA9	XM_047431999.1	c.-937T>C		5_prime_UTR_variant	1/14

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21600 AN: 151588 Hom.: 2004 Cov.: 30

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.142 AC: 21595 AN: 151706 Hom.: 2004 Cov.: 30 AF XY: 0.141 AC XY: 10462 AN XY: 74136

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.150

Alfa AF: 0.189 Hom.: 3862

Bravo AF: 0.132

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267734; hg19: chr1-150951477;