rs2447822

Variant names:

• chr5-127600404-A-G
• rs2447822

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 0.07 in 152,186 control chromosomes in the GnomAD database, including 430 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 0.070 (430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 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: 0.0700 AC: 10652 AN: 152068 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.0700 AC: 10654 AN: 152186 Hom.: 430 Cov.: 32 AF XY: 0.0712 AC XY: 5301 AN XY: 74404

African (AFR) AF: 0.0370 AC: 1535 AN: 41532

American (AMR) AF: 0.102 AC: 1552 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3470

East Asian (EAS) AF: 0.140 AC: 723 AN: 5172

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4818

European-Finnish (FIN) AF: 0.0577 AC: 611 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5222 AN: 68008

Other (OTH) AF: 0.0873 AC: 184 AN: 2108

Alfa AF: 0.0793 Hom.: 581

Bravo AF: 0.0750

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.80
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs2447822; hg19: chr5-126936096;