chr9-22137686-T-G

Position:

• chr9-22137686-T-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 0.274 in 152,018 control chromosomes in the GnomAD database, including 5,690 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 0.27 (5690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 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: 0.274 AC: 41565 AN: 151898 Hom.: 5687 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.274 AC: 41577 AN: 152018 Hom.: 5690 Cov.: 31 AF XY: 0.275 AC XY: 20407 AN XY: 74308

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.297

Alfa AF: 0.274 Hom.: 10240

Bravo AF: 0.274

Asia WGS AF: 0.339 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7018475; hg19: chr9-22137685;