rs1619450

Variant names:

• chr9-91406873-A-G
• rs1619450

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 0.0696 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0696 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

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0850

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0865

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0802 Hom.: 565

Bravo AF: 0.0661

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1619450; hg19: chr9-94169155;