rs1187321

chr9-84668116-T-Achr9-84668116-T-Cchr9-84668116-T-G

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 0.714 in 152,188 control chromosomes in the GnomAD database, including 40,219 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 0.71 (40219 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 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: 0.714 AC: 108569 AN: 152070 Hom.: 40208 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.714 AC: 108634 AN: 152188 Hom.: 40219 Cov.: 33 AF XY: 0.717 AC XY: 53354 AN XY: 74404

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.740

Alfa AF: 0.697 Hom.: 2277

Bravo AF: 0.699

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1187321; hg19: chr9-87283031;