rs10491923

chr9-74334264-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 0.22 in 152,034 control chromosomes in the GnomAD database, including 4,297 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 (4297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.220 AC: 33384 AN: 151916 Hom.: 4281 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.220 AC: 33442 AN: 152034 Hom.: 4297 Cov.: 32 AF XY: 0.222 AC XY: 16454 AN XY: 74284

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.231

Alfa AF: 0.257 Hom.: 6849

Bravo AF: 0.215

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.9
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491923; hg19: chr9-76949180;