rs1687390

chr9-114327608-G-A

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 0.126 in 149,142 control chromosomes in the GnomAD database, including 86 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 0.13 (86 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18700 AN: 149026 Hom.: 86 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0917

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.00253

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.126 AC: 18726 AN: 149142 Hom.: 86 Cov.: 30 AF XY: 0.122 AC XY: 8878 AN XY: 72930

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.00253

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0691

Gnomad4 OTH AF: 0.122

Alfa AF: 0.110 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	16
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1687390; hg19: chr9-117089888;