rs2383811

chr9-29416255-G-Achr9-29416255-G-C

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 0.885 in 150,756 control chromosomes in the GnomAD database, including 59,086 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 0.88 (59086 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.885 AC: 133292 AN: 150636 Hom.: 59030 Cov.: 29

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.885 AC: 133406 AN: 150756 Hom.: 59086 Cov.: 29 AF XY: 0.886 AC XY: 65248 AN XY: 73624

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.889

Alfa AF: 0.878 Hom.: 26687

Bravo AF: 0.886

Asia WGS AF: 0.923 AC: 3210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.0
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383811; hg19: chr9-29416253;