rs1114559

Variant names:

• chr9-79808879-G-A
• rs1114559

Your query was ambiguous. Multiple possible variants found:

• chr9-79808879-G-A
• chr9-79808879-G-T

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 0.811 in 152,088 control chromosomes in the GnomAD database, including 50,466 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 0.81 (50466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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: 0.811 AC: 123273 AN: 151970 Hom.: 50422 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.811 AC: 123368 AN: 152088 Hom.: 50466 Cov.: 31 AF XY: 0.808 AC XY: 60030 AN XY: 74332

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.808

Alfa AF: 0.793 Hom.: 14788

Bravo AF: 0.812

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1114559; hg19: chr9-82423794; COSMIC: COSV60364169;