rs2025126

Variant names:

• chr9-35696628-G-A
• rs2025126

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 0.225 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
• Publications: 31 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0976 AC: 4054 AN: 41532

American (AMR) AF: 0.286 AC: 4369 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1677 AN: 5184

South Asian (SAS) AF: 0.199 AC: 958 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2479 AN: 10598

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19023 AN: 67992

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.251 Hom.: 2450

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2025126; hg19: chr9-35696625;