15-22832212-A-G

Variant names:

• chr15-22832212-A-G
• rs4778334

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 0.722 in 151,822 control chromosomes in the GnomAD database, including 40,322 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 0.72 (40322 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.722 AC: 109496 AN: 151704 Hom.: 40306 Cov.: 30

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.722 AC: 109557 AN: 151822 Hom.: 40322 Cov.: 30 AF XY: 0.729 AC XY: 54061 AN XY: 74184

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.705

Alfa AF: 0.748 Hom.: 63119

Bravo AF: 0.712

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778334; hg19: chr15-23040856;