chr7-100616392-A-G

Variant names:

• chr7-100616392-A-G
• rs7786877

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 0.225 in 151,938 control chromosomes in the GnomAD database, including 3,953 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 0.22 (3953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34136 AN: 151828 Hom.: 3945 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.225 AC: 34175 AN: 151938 Hom.: 3953 Cov.: 31 AF XY: 0.222 AC XY: 16492 AN XY: 74256

African (AFR) AF: 0.187 AC: 7735 AN: 41454

American (AMR) AF: 0.200 AC: 3047 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.112 AC: 581 AN: 5166

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4810

European-Finnish (FIN) AF: 0.259 AC: 2723 AN: 10522

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17219 AN: 67968

Other (OTH) AF: 0.231 AC: 487 AN: 2104

Alfa AF: 0.241 Hom.: 5954

Bravo AF: 0.218

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7786877; hg19: chr7-100214015;