9-114819660-T-C

Variant names:

• chr9-114819660-T-C
• rs2145929

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 0.216 in 152,094 control chromosomes in the GnomAD database, including 4,197 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 0.22 (4197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32734 AN: 151976 Hom.: 4184 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.216 AC: 32786 AN: 152094 Hom.: 4197 Cov.: 32 AF XY: 0.214 AC XY: 15893 AN XY: 74356

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.198

Alfa AF: 0.146 Hom.: 973

Bravo AF: 0.227

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2145929; hg19: chr9-117581940;