9-24530617-C-G

Variant names:

• chr9-24530617-C-G
• rs2805064

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.202 in 152,108 control chromosomes in the GnomAD database, including 3,742 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 0.20 (3742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30645 AN: 151990 Hom.: 3738 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.202 AC: 30674 AN: 152108 Hom.: 3742 Cov.: 32 AF XY: 0.202 AC XY: 15021 AN XY: 74354

African (AFR) AF: 0.0831 AC: 3452 AN: 41538

American (AMR) AF: 0.224 AC: 3422 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3464

East Asian (EAS) AF: 0.183 AC: 943 AN: 5156

South Asian (SAS) AF: 0.144 AC: 693 AN: 4820

European-Finnish (FIN) AF: 0.311 AC: 3289 AN: 10588

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17888 AN: 67962

Other (OTH) AF: 0.194 AC: 410 AN: 2110

Alfa AF: 0.223 Hom.: 565

Bravo AF: 0.191

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	16
DANN	Benign	0.61
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs2805064; hg19: chr9-24530615;