rs1619450

Variant names:

• chr9-91406873-A-G
• rs1619450

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 0.0696 in 152,182 control chromosomes in the GnomAD database, including 462 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 (462 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0928 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: 0.0696 AC: 10577 AN: 152064 Hom.: 463 Cov.: 31

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0696 AC: 10591 AN: 152182 Hom.: 462 Cov.: 31 AF XY: 0.0717 AC XY: 5335 AN XY: 74384

African (AFR) AF: 0.0180 AC: 749 AN: 41538

American (AMR) AF: 0.0970 AC: 1483 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3472

East Asian (EAS) AF: 0.0850 AC: 440 AN: 5174

South Asian (SAS) AF: 0.0877 AC: 423 AN: 4822

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10584

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5883 AN: 67978

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0787 Hom.: 713

Bravo AF: 0.0661

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.35
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1619450; hg19: chr9-94169155;