rs2047822

Positions:

• chr15-69272569-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;