rs1329853

Variant names:

• chr9-24528894-A-G
• rs1329853

Variant summary

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

The variant allele was found at a frequency of 0.277 in 150,286 control chromosomes in the GnomAD database, including 5,814 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 0.28 (5814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41584 AN: 150168 Hom.: 5780 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.141

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.277 AC: 41681 AN: 150286 Hom.: 5814 Cov.: 32 AF XY: 0.275 AC XY: 20178 AN XY: 73472

African (AFR) AF: 0.240 AC: 9793 AN: 40868

American (AMR) AF: 0.279 AC: 4223 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 659 AN: 3454

East Asian (EAS) AF: 0.207 AC: 1048 AN: 5074

South Asian (SAS) AF: 0.158 AC: 746 AN: 4712

European-Finnish (FIN) AF: 0.338 AC: 3546 AN: 10480

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.310 AC: 20834 AN: 67300

Other (OTH) AF: 0.279 AC: 583 AN: 2088

Alfa AF: 0.289 Hom.: 3993

Bravo AF: 0.272

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1329853; hg19: chr9-24528892;