9-97875057-C-T

Position:

• chr9-97875057-C-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 0.502 in 152,016 control chromosomes in the GnomAD database, including 20,205 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 0.50 (20205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76202 AN: 151898 Hom.: 20172 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.502 AC: 76272 AN: 152016 Hom.: 20205 Cov.: 32 AF XY: 0.509 AC XY: 37845 AN XY: 74332

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.473

Alfa AF: 0.420 Hom.: 13733

Bravo AF: 0.507

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	4.9
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: rs10119795; hg19: chr9-100637339;