9-27075717-A-G

Position:

• chr9-27075717-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 0.323 in 152,026 control chromosomes in the GnomAD database, including 8,924 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 (8924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.323 AC: 49064 AN: 151908 Hom.: 8890 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.323 AC: 49161 AN: 152026 Hom.: 8924 Cov.: 32 AF XY: 0.332 AC XY: 24708 AN XY: 74314

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.322

Alfa AF: 0.264 Hom.: 906

Bravo AF: 0.328

Asia WGS AF: 0.554 AC: 1923 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	1.4
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1577330; hg19: chr9-27075715;