rs2447822

Positions:

• chr5-127600404-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 0.07 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;