9-25667521-G-C

Variant names:

• chr9-25667521-G-C
• rs13290968

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 0.136 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.120 AC: 4977 AN: 41480

American (AMR) AF: 0.121 AC: 1850 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 330 AN: 3462

East Asian (EAS) AF: 0.0512 AC: 265 AN: 5172

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2142 AN: 10530

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10321 AN: 67916

Other (OTH) AF: 0.132 AC: 279 AN: 2110

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs13290968; hg19: chr9-25667519;