9-27589659-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 0.844 in 152,250 control chromosomes in the GnomAD database, including 54,362 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 0.84 (54362 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.845 AC: 128481 AN: 152132 Hom.: 54338 Cov.: 34

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.844 AC: 128555 AN: 152250 Hom.: 54362 Cov.: 34 AF XY: 0.847 AC XY: 63081 AN XY: 74446

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.845

Alfa AF: 0.838 Hom.: 33486

Bravo AF: 0.845

Asia WGS AF: 0.936 AC: 3257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs696826; hg19: chr9-27589657; COSMIC: COSV60346998;