rs1228439

Variant names:

• chr9-129589899-A-G
• rs1228439

Your query was ambiguous. Multiple possible variants found:

• chr9-129589899-A-G
• chr9-129589899-A-T

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 0.556 in 152,042 control chromosomes in the GnomAD database, including 24,027 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 0.56 (24027 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 2 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.556 AC: 84500 AN: 151924 Hom.: 24007 Cov.: 33

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.556 AC: 84569 AN: 152042 Hom.: 24027 Cov.: 33 AF XY: 0.557 AC XY: 41361 AN XY: 74306

African (AFR) AF: 0.471 AC: 19534 AN: 41466

American (AMR) AF: 0.615 AC: 9385 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3466

East Asian (EAS) AF: 0.782 AC: 4051 AN: 5182

South Asian (SAS) AF: 0.451 AC: 2168 AN: 4812

European-Finnish (FIN) AF: 0.629 AC: 6633 AN: 10538

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39430 AN: 67988

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.572 Hom.: 107387

Bravo AF: 0.558

Asia WGS AF: 0.563 AC: 1957 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	1.6
DANN	Benign	0.28
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1228439; hg19: chr9-132352178; COSMIC: COSV69038571;