9-22130516-G-A

Position:

• chr9-22130516-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 0.125 in 151,996 control chromosomes in the GnomAD database, including 1,549 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 0.13 (1549 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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 (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19033 AN: 151878 Hom.: 1544 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.125 AC: 19059 AN: 151996 Hom.: 1549 Cov.: 33 AF XY: 0.127 AC XY: 9461 AN XY: 74284

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0955 Hom.: 331

Bravo AF: 0.131

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10965245; hg19: chr9-22130515;