rs2060439

Variant names:

• chr9-26242138-G-A
• rs2060439

Your query was ambiguous. Multiple possible variants found:

• chr9-26242138-G-A
• chr9-26242138-G-C
• chr9-26242138-G-T

Variant summary

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

The variant allele was found at a frequency of 0.0843 in 152,080 control chromosomes in the GnomAD database, including 1,397 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 0.084 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.0842 AC: 12795 AN: 151962 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.0843 AC: 12823 AN: 152080 Hom.: 1397 Cov.: 32 AF XY: 0.0914 AC XY: 6796 AN XY: 74352

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.0114

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0916

Alfa AF: 0.0355 Hom.: 78

Bravo AF: 0.100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060439; hg19: chr9-26242136;