chr9-86912543-A-G

Variant names:

• chr9-86912543-A-G
• rs11141597

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 0.0267 in 152,258 control chromosomes in the GnomAD database, including 88 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 0.027 (88 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0501 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: 0.0266 AC: 4053 AN: 152140 Hom.: 85 Cov.: 33

Gnomad AFR AF: 0.00664

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0267 AC: 4061 AN: 152258 Hom.: 88 Cov.: 33 AF XY: 0.0284 AC XY: 2116 AN XY: 74454

Gnomad4 AFR AF: 0.00662

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0318

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.0197 Hom.: 13

Bravo AF: 0.0241

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11141597; hg19: chr9-89527458;