chr9-111095057-T-C

Position:

• chr9-111095057-T-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 0.182 in 152,198 control chromosomes in the GnomAD database, including 2,692 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 0.18 (2692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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: 0.182 AC: 27702 AN: 152080 Hom.: 2684 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.182 AC: 27733 AN: 152198 Hom.: 2692 Cov.: 32 AF XY: 0.175 AC XY: 12994 AN XY: 74398

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.194

Alfa AF: 0.191 Hom.: 3091

Bravo AF: 0.189

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7861175; hg19: chr9-113857337;