chr9-89765957-A-C

Position:

• chr9-89765957-A-C

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 0.0705 in 152,234 control chromosomes in the GnomAD database, including 492 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 0.071 (492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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 (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0706 AC: 10738 AN: 152116 Hom.: 492 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0705 AC: 10739 AN: 152234 Hom.: 492 Cov.: 32 AF XY: 0.0690 AC XY: 5138 AN XY: 74432

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.0598

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0750

Gnomad4 FIN AF: 0.0621

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0980 Hom.: 694

Bravo AF: 0.0655

Asia WGS AF: 0.0330 AC: 113 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	0.84
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265930; hg19: chr9-92467404;