9-26242138-G-A

Variant names:

• chr9-26242138-G-A
• rs2060439

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 0.0843 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.113 AC: 4685 AN: 41488

American (AMR) AF: 0.188 AC: 2872 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3466

East Asian (EAS) AF: 0.504 AC: 2600 AN: 5154

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4806

European-Finnish (FIN) AF: 0.0114 AC: 121 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0162 AC: 1103 AN: 67966

Other (OTH) AF: 0.0916 AC: 193 AN: 2108

Alfa AF: 0.0355 Hom.: 78

Bravo AF: 0.100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2060439; hg19: chr9-26242136;