9-120099019-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 0.179 in 152,182 control chromosomes in the GnomAD database, including 2,866 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 (2866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669

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 (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.179 AC: 27164 AN: 152062 Hom.: 2867 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.179 AC: 27169 AN: 152182 Hom.: 2866 Cov.: 32 AF XY: 0.179 AC XY: 13317 AN XY: 74388

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.173

Alfa AF: 0.210 Hom.: 4941

Bravo AF: 0.171

Asia WGS AF: 0.271 AC: 940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16909449; hg19: chr9-122861297;