rs3754210

Positions:

• chr1-150981785-G-T

Variant summary

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

The XM_047431983.1(ANXA9):​c.-192-516G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,220 control chromosomes in the GnomAD database, including 3,519 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 0.18 (3519 hom., cov: 33)
• Consequence: ANXA9 XM_047431983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

Genes affected

ANXA9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANXA9	XM_047431983.1	c.-192-516G>T		intron_variant
ANXA9	XM_047431984.1	c.-193+118G>T		intron_variant
ANXA9	XM_047431986.1	c.-193+118G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26865 AN: 152102 Hom.: 3502 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26926 AN: 152220 Hom.: 3519 Cov.: 33 AF XY: 0.175 AC XY: 13004 AN XY: 74424

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.0928

Gnomad4 OTH AF: 0.160

Alfa AF: 0.120 Hom.: 690

Bravo AF: 0.189

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754210; hg19: chr1-150954261;