rs10448253

chr9-117667193-G-A

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 0.0593 in 152,220 control chromosomes in the GnomAD database, including 331 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 0.059 (331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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 = 0.111 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: 0.0594 AC: 9034 AN: 152102 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0593 AC: 9030 AN: 152220 Hom.: 331 Cov.: 32 AF XY: 0.0610 AC XY: 4537 AN XY: 74416

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.0780

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0722 Hom.: 203

Bravo AF: 0.0511

Asia WGS AF: 0.0680 AC: 234 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	3.5
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10448253; hg19: chr9-120429471;