9-87142805-G-T

Position:

• chr9-87142805-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 0.853 in 151,728 control chromosomes in the GnomAD database, including 55,416 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 0.85 (55416 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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: 0.853 AC: 129293 AN: 151608 Hom.: 55372 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.853 AC: 129396 AN: 151728 Hom.: 55416 Cov.: 30 AF XY: 0.856 AC XY: 63469 AN XY: 74130

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.861

Alfa AF: 0.776 Hom.: 2222

Bravo AF: 0.862

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.95
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277729; hg19: chr9-89757720;