9-110850339-G-C

Position:

• chr9-110850339-G-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 0.271 in 151,944 control chromosomes in the GnomAD database, including 5,592 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 0.27 (5592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.271 AC: 41184 AN: 151826 Hom.: 5589 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.271 AC: 41230 AN: 151944 Hom.: 5592 Cov.: 32 AF XY: 0.275 AC XY: 20461 AN XY: 74270

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.257

Alfa AF: 0.136 Hom.: 240

Bravo AF: 0.265

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.82
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531003; hg19: chr9-113612619;