rs2025126

Positions:

• chr9-35696628-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 0.225 in 152,206 control chromosomes in the GnomAD database, including 4,416 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 0.23 (4416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.226 AC: 34306 AN: 152088 Hom.: 4421 Cov.: 31

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.225 AC: 34285 AN: 152206 Hom.: 4416 Cov.: 31 AF XY: 0.224 AC XY: 16696 AN XY: 74402

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.225

Alfa AF: 0.255 Hom.: 2101

Bravo AF: 0.225

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.93
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025126; hg19: chr9-35696625;