9-25667521-G-C

Position:

• chr9-25667521-G-C

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 0.136 in 151,948 control chromosomes in the GnomAD database, including 1,436 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 0.14 (1436 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 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: 0.136 AC: 20629 AN: 151830 Hom.: 1435 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.136 AC: 20643 AN: 151948 Hom.: 1436 Cov.: 33 AF XY: 0.136 AC XY: 10083 AN XY: 74250

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.0512

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0651 Hom.: 87

Bravo AF: 0.130

Asia WGS AF: 0.0610 AC: 212 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.57
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290968; hg19: chr9-25667519;