9-26789942-A-G

Position:

• chr9-26789942-A-G

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 0.324 in 149,664 control chromosomes in the GnomAD database, including 8,450 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 0.32 (8450 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.325 AC: 48550 AN: 149550 Hom.: 8452 Cov.: 26

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.324 AC: 48550 AN: 149664 Hom.: 8450 Cov.: 26 AF XY: 0.321 AC XY: 23417 AN XY: 72892

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.374

Alfa AF: 0.363 Hom.: 15446

Bravo AF: 0.313

Asia WGS AF: 0.221 AC: 769 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1889899; hg19: chr9-26789940; COSMIC: COSV73098443;