rs2169325

chr9-24911870-G-Achr9-24911870-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 0.256 in 152,126 control chromosomes in the GnomAD database, including 5,604 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 0.26 (5604 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.257 AC: 39033 AN: 152008 Hom.: 5619 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.256 AC: 39017 AN: 152126 Hom.: 5604 Cov.: 33 AF XY: 0.258 AC XY: 19165 AN XY: 74348

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.304

Alfa AF: 0.292 Hom.: 3255

Bravo AF: 0.256

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.45
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169325; hg19: chr9-24911868;