rs17724552

chr9-107238073-G-Achr9-107238073-G-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 0.0983 in 152,112 control chromosomes in the GnomAD database, including 869 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 0.098 (869 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 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: 0.0983 AC: 14936 AN: 151994 Hom.: 868 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0983 AC: 14951 AN: 152112 Hom.: 869 Cov.: 33 AF XY: 0.0971 AC XY: 7220 AN XY: 74342

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.115

Alfa AF: 0.123 Hom.: 1691

Bravo AF: 0.0963

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.9
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17724552; hg19: chr9-110000354;