rs2447822

Variant names:

• chr5-127600404-A-G
• rs2447822

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 0.07 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.0577

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.0873

Alfa AF: 0.0791 Hom.: 439

Bravo AF: 0.0750

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2447822; hg19: chr5-126936096;