rs2047822

Variant names:

• chr15-69272569-G-C
• rs2047822

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 0.125 in 152,260 control chromosomes in the GnomAD database, including 1,260 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 0.12 (1260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 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: 0.125 AC: 18986 AN: 152142 Hom.: 1258 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.125 AC: 18997 AN: 152260 Hom.: 1260 Cov.: 33 AF XY: 0.123 AC XY: 9180 AN XY: 74442

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.128

Alfa AF: 0.126 Hom.: 156

Bravo AF: 0.124

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047822; hg19: chr15-69564908;