9-26580069-G-A

Variant names:

• chr9-26580069-G-A
• rs996414

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 0.762 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.559 AC: 23145 AN: 41380

American (AMR) AF: 0.856 AC: 13043 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4715 AN: 5170

South Asian (SAS) AF: 0.817 AC: 3943 AN: 4826

European-Finnish (FIN) AF: 0.830 AC: 8777 AN: 10574

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56790 AN: 67980

Other (OTH) AF: 0.777 AC: 1645 AN: 2116

Alfa AF: 0.815 Hom.: 81732

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs996414; hg19: chr9-26580067;