rs10448208

Variant names:

• chr9-21378326-G-A
• rs10448208

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 0.218 in 151,918 control chromosomes in the GnomAD database, including 4,836 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 0.22 (4836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.218 AC: 33094 AN: 151800 Hom.: 4817 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.218 AC: 33156 AN: 151918 Hom.: 4836 Cov.: 32 AF XY: 0.217 AC XY: 16106 AN XY: 74212

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.189

Alfa AF: 0.175 Hom.: 762

Bravo AF: 0.236

Asia WGS AF: 0.276 AC: 955 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10448208; hg19: chr9-21378325;