9-26580069-G-A

Position:

• chr9-26580069-G-A

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 0.762 in 151,948 control chromosomes in the GnomAD database, including 45,454 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 0.76 (45454 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115727 AN: 151830 Hom.: 45422 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.762 AC: 115807 AN: 151948 Hom.: 45454 Cov.: 31 AF XY: 0.767 AC XY: 56943 AN XY: 74256

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.777

Alfa AF: 0.823 Hom.: 65737

Bravo AF: 0.753

Asia WGS AF: 0.867 AC: 3018 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	0.26
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996414; hg19: chr9-26580067;