chr7-82569857-G-A

Variant names:

• chr7-82569857-G-A
• rs2214733

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 0.926 in 152,228 control chromosomes in the GnomAD database, including 65,426 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 0.93 (65426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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: 0.926 AC: 140911 AN: 152110 Hom.: 65385 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.926 AC: 141007 AN: 152228 Hom.: 65426 Cov.: 32 AF XY: 0.925 AC XY: 68859 AN XY: 74418

African (AFR) AF: 0.984 AC: 40888 AN: 41538

American (AMR) AF: 0.889 AC: 13604 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3213 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4642 AN: 5166

South Asian (SAS) AF: 0.896 AC: 4324 AN: 4824

European-Finnish (FIN) AF: 0.915 AC: 9695 AN: 10594

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61595 AN: 68018

Other (OTH) AF: 0.919 AC: 1945 AN: 2116

Alfa AF: 0.912 Hom.: 103996

Bravo AF: 0.927

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2214733; hg19: chr7-82199173;