chr15-48366591-A-G

Variant names:

• chr15-48366591-A-G
• rs1872304

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.703 in 152,062 control chromosomes in the GnomAD database, including 39,600 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 0.70 (39600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106933 AN: 151944 Hom.: 39603 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.703 AC: 106971 AN: 152062 Hom.: 39600 Cov.: 32 AF XY: 0.702 AC XY: 52190 AN XY: 74334

African (AFR) AF: 0.473 AC: 19603 AN: 41446

American (AMR) AF: 0.756 AC: 11548 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2794 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2430 AN: 5160

South Asian (SAS) AF: 0.659 AC: 3179 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8528 AN: 10574

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56332 AN: 68008

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.668 Hom.: 13347

Bravo AF: 0.692

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs1872304; hg19: chr15-48658788;