rs7786877

chr7-100616392-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 0.225 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.225 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

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.231

Alfa AF: 0.245 Hom.: 4099

Bravo AF: 0.218

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.70
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7786877; hg19: chr7-100214015;