chr9-22134303-C-G

Position:

• chr9-22134303-C-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 0.384 in 151,988 control chromosomes in the GnomAD database, including 11,822 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 0.38 (11822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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 = 0.604 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: 0.385 AC: 58404 AN: 151870 Hom.: 11821 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.384 AC: 58412 AN: 151988 Hom.: 11822 Cov.: 32 AF XY: 0.388 AC XY: 28822 AN XY: 74274

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.425

Alfa AF: 0.399 Hom.: 1514

Bravo AF: 0.377

Asia WGS AF: 0.540 AC: 1877 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	0.60
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7019437; hg19: chr9-22134302; COSMIC: COSV60341856;