chr7-22107222-A-G

Position:

• chr7-22107222-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 0.249 in 152,060 control chromosomes in the GnomAD database, including 5,397 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 0.25 (5397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 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: 0.249 AC: 37812 AN: 151940 Hom.: 5384 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.249 AC: 37863 AN: 152060 Hom.: 5397 Cov.: 32 AF XY: 0.254 AC XY: 18863 AN XY: 74346

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.243

Alfa AF: 0.199 Hom.: 6636

Bravo AF: 0.249

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7793103; hg19: chr7-22146840;