chr9-96122862-G-A

Position:

• chr9-96122862-G-A

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 0.747 in 152,212 control chromosomes in the GnomAD database, including 43,205 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 0.75 (43205 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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 = 0.894 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: 0.747 AC: 113560 AN: 152094 Hom.: 43140 Cov.: 34

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.747 AC: 113688 AN: 152212 Hom.: 43205 Cov.: 34 AF XY: 0.748 AC XY: 55649 AN XY: 74406

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.742

Alfa AF: 0.688 Hom.: 48561

Bravo AF: 0.758

Asia WGS AF: 0.776 AC: 2699 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	7.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4743558; hg19: chr9-98885144;