rs1114559

chr9-79808879-G-Achr9-79808879-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;