rs7793103

Variant names:

• chr7-22107222-A-G
• rs7793103

Your query was ambiguous. Multiple possible variants found:

• chr7-22107222-A-G
• chr7-22107222-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.341 AC: 14114 AN: 41426

American (AMR) AF: 0.165 AC: 2522 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3074 AN: 5176

South Asian (SAS) AF: 0.243 AC: 1176 AN: 4830

European-Finnish (FIN) AF: 0.263 AC: 2787 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12825 AN: 67972

Other (OTH) AF: 0.243 AC: 513 AN: 2108

Alfa AF: 0.206 Hom.: 15362

Bravo AF: 0.249

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.63
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7793103; hg19: chr7-22146840;