rs10901296

chr9-130890269-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 0.0465 in 152,238 control chromosomes in the GnomAD database, including 233 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 0.046 (233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0694 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: 0.0466 AC: 7082 AN: 152120 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0465 AC: 7079 AN: 152238 Hom.: 233 Cov.: 32 AF XY: 0.0433 AC XY: 3220 AN XY: 74446

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0281

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0637 Hom.: 177

Bravo AF: 0.0459

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.045
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10901296; hg19: chr9-133765656;