9-104943907-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 0.173 in 152,012 control chromosomes in the GnomAD database, including 2,819 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 0.17 (2819 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.173 AC: 26311 AN: 151894 Hom.: 2824 Cov.: 31

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.173 AC: 26308 AN: 152012 Hom.: 2819 Cov.: 31 AF XY: 0.178 AC XY: 13242 AN XY: 74270

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.175

Alfa AF: 0.185 Hom.: 520

Bravo AF: 0.162

Asia WGS AF: 0.289 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.95
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2487030; hg19: chr9-107706188;