7-80227095-T-C

Variant names:

• chr7-80227095-T-C
• rs2886609

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 0.54 in 152,078 control chromosomes in the GnomAD database, including 23,105 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 0.54 (23105 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82041 AN: 151960 Hom.: 23094 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.540 AC: 82078 AN: 152078 Hom.: 23105 Cov.: 33 AF XY: 0.541 AC XY: 40193 AN XY: 74342

African (AFR) AF: 0.378 AC: 15697 AN: 41472

American (AMR) AF: 0.606 AC: 9262 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2266 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4172 AN: 5188

South Asian (SAS) AF: 0.636 AC: 3062 AN: 4816

European-Finnish (FIN) AF: 0.558 AC: 5903 AN: 10578

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39681 AN: 67962

Other (OTH) AF: 0.588 AC: 1243 AN: 2114

Alfa AF: 0.577 Hom.: 104528

Bravo AF: 0.539

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.2
DANN	Benign	0.81
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2886609; hg19: chr7-79856411;