rs10448253

Variant names:

• chr9-117667193-G-A
• rs10448253

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0235 AC: 975 AN: 41546

American (AMR) AF: 0.0483 AC: 738 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5174

South Asian (SAS) AF: 0.119 AC: 572 AN: 4824

European-Finnish (FIN) AF: 0.0981 AC: 1040 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5302 AN: 67992

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0692 Hom.: 277

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10448253; hg19: chr9-120429471;