chr9-24911870-G-A

Variant names:

• chr9-24911870-G-A
• rs2169325

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 0.256 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.127 AC: 5278 AN: 41538

American (AMR) AF: 0.314 AC: 4794 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1956 AN: 5154

South Asian (SAS) AF: 0.312 AC: 1507 AN: 4826

European-Finnish (FIN) AF: 0.266 AC: 2810 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20302 AN: 67988

Other (OTH) AF: 0.304 AC: 641 AN: 2108

Alfa AF: 0.292 Hom.: 3629

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2169325; hg19: chr9-24911868;